17-30117165-A-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_032141.4(NSRP1):c.20+302A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 708,838 control chromosomes in the GnomAD database, including 84,758 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 14884 hom., cov: 31)

Exomes 𝑓: 0.49 ( 69874 hom. )

Consequence

NSRP1
NM_032141.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.939

Publications

184 publications found

Variant links:

Genes affected

NSRP1 (HGNC:25305): (nuclear speckle splicing regulatory protein 1) Enables mRNA binding activity. Involved in developmental process and regulation of alternative mRNA splicing, via spliceosome. Located in nuclear speck. Part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]

NSRP1 links:

MIR423 (HGNC:31880): (microRNA 423) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR423 links:

hsa-mir-423 (HGNC:):

hsa-mir-423 links:

MIR3184 (HGNC:38182): (microRNA 3184) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR3184 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 17-30117165-A-C is Benign according to our data. Variant chr17-30117165-A-C is described in ClinVar as Benign. ClinVar VariationId is 1221211.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032141.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NSRP1	NM_032141.4	MANE Select	c.20+302A>C	intron	N/A	NP_115517.1	Q9H0G5
NSRP1	NM_001261467.2		c.-49+302A>C	intron	N/A	NP_001248396.1	A0A024QZ33
MIR423	NR_029945.1		n.87A>C	non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NSRP1	ENST00000247026.10	TSL:1 MANE Select	c.20+302A>C	intron	N/A	ENSP00000247026.5	Q9H0G5
NSRP1	ENST00000612959.4	TSL:1	c.-49+302A>C	intron	N/A	ENSP00000477862.1	A0A024QZ33
NSRP1	ENST00000394826.8	TSL:1	n.20+302A>C	intron	N/A	ENSP00000378303.4	H7BYM1

Frequencies

GnomAD3 genomes

AF:

0.424

AC:

64399

AN:

151734

Hom.:

14886

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.459

Gnomad AMR

AF:

0.519

Gnomad ASJ

AF:

0.569

Gnomad EAS

AF:

0.806

Gnomad SAS

AF:

0.554

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.545

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.468

GnomAD2 exomes

AF:

0.500

AC:

80035

AN:

159944

AF XY:

0.504

show subpopulations

Gnomad AFR exome

AF:

0.262

Gnomad AMR exome

AF:

0.569

Gnomad ASJ exome

AF:

0.562

Gnomad EAS exome

AF:

0.792

Gnomad FIN exome

AF:

0.439

Gnomad NFE exome

AF:

0.450

Gnomad OTH exome

AF:

0.504

GnomAD4 exome

AF:

0.490

AC:

272803

AN:

556986

Hom.:

69874

Cov.:

AF XY:

0.493

AC XY:

148252

AN XY:

300794

show subpopulations

African (AFR)

AF:

0.267

AC:

4052

AN:

15162

American (AMR)

AF:

0.562

AC:

18974

AN:

33788

Ashkenazi Jewish (ASJ)

AF:

0.556

AC:

10747

AN:

19312

East Asian (EAS)

AF:

0.801

AC:

26027

AN:

32490

South Asian (SAS)

AF:

0.543

AC:

33690

AN:

62066

European-Finnish (FIN)

AF:

0.435

AC:

21322

AN:

48996

Middle Eastern (MID)

AF:

0.557

AC:

1534

AN:

2756

European-Non Finnish (NFE)

AF:

0.455

AC:

142123

AN:

312492

Other (OTH)

AF:

0.479

AC:

14334

AN:

29924

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

6884

13768

20653

27537

34421

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

832

1664

2496

3328

4160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.424

AC:

64399

AN:

151852

Hom.:

14884

Cov.:

AF XY:

0.432

AC XY:

32082

AN XY:

74178

show subpopulations

African (AFR)

AF:

0.261

AC:

10796

AN:

41398

American (AMR)

AF:

0.519

AC:

7913

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.569

AC:

1974

AN:

3470

East Asian (EAS)

AF:

0.808

AC:

4167

AN:

5160

South Asian (SAS)

AF:

0.553

AC:

2659

AN:

4806

European-Finnish (FIN)

AF:

0.430

AC:

4529

AN:

10532

Middle Eastern (MID)

AF:

0.524

AC:

152

AN:

290

European-Non Finnish (NFE)

AF:

0.454

AC:

30809

AN:

67924

Other (OTH)

AF:

0.465

AC:

982

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1759

3518

5276

7035

8794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.449

Hom.:

44252

Bravo

AF:

0.427

Asia WGS

AF:

0.589

AC:

2049

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

0.94

PromoterAI

0.021

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over