Genetic Variant SNRNP70:c.147+1120C>T (chr19-49087681-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003089.6(SNRNP70):c.147+1120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,000 control chromosomes in the GnomAD database, including 9,626 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.35 ( 9626 hom., cov: 32)

Exomes 𝑓: 0.42 ( 0 hom. )

Consequence

SNRNP70
NM_003089.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.56

Publications

13 publications found

Variant links:

Genes affected

SNRNP70 (HGNC:11150): (small nuclear ribonucleoprotein U1 subunit 70) Enables U1 snRNA binding activity. Involved in mRNA splicing, via spliceosome and regulation of RNA splicing. Located in nucleoplasm. Part of U1 snRNP and spliceosomal complex. Implicated in disease of mental health and systemic lupus erythematosus. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]

SNRNP70 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003089.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRNP70	NM_003089.6	MANE Select	c.147+1120C>T		intron	N/A	NP_003080.2
	SNRNP70	NM_001301069.2		c.147+1120C>T		intron	N/A	NP_001287998.1	P08621-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SNRNP70	ENST00000598441.6	TSL:1 MANE Select	c.147+1120C>T	intron	N/A	ENSP00000472998.1	P08621-1
SNRNP70	ENST00000595231.5	TSL:1	n.147+1120C>T	intron	N/A	ENSP00000471006.1	P08621-3
SNRNP70	ENST00000601411.1	TSL:5	c.-148C>T	5_prime_UTR	Exon 2 of 5	ENSP00000468828.1	M0QX04

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52601

AN:

151870

Hom.:

9625

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.415

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.0751

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.403

Gnomad OTH

AF:

0.356

GnomAD4 exome

AF:

0.417

AC:

AN:

Hom.:

Cov.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.415

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.346

AC:

52616

AN:

151988

Hom.:

9626

Cov.:

AF XY:

0.341

AC XY:

25321

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.301

AC:

12486

AN:

41458

American (AMR)

AF:

0.261

AC:

3982

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.409

AC:

1414

AN:

3460

East Asian (EAS)

AF:

0.0747

AC:

387

AN:

5180

South Asian (SAS)

AF:

0.459

AC:

2212

AN:

4820

European-Finnish (FIN)

AF:

0.332

AC:

3506

AN:

10546

Middle Eastern (MID)

AF:

0.418

AC:

123

AN:

294

European-Non Finnish (NFE)

AF:

0.403

AC:

27384

AN:

67962

Other (OTH)

AF:

0.353

AC:

744

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1736

3471

5207

6942

8678

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<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:

0.379

Hom.:

52054

Bravo

AF:

0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.43

(source)

DANN

Benign

0.60

PhyloP100

-1.6

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