Genetic Variant RN7SL685P:n.9C>T (chr8-100957891-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 ENST00000476271.3(RN7SL685P):n.9C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,956 control chromosomes in the GnomAD database, including 33,082 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 0.65 ( 33074 hom., cov: 31)

Exomes 𝑓: 0.66 ( 8 hom. )

Consequence

RN7SL685P
ENST00000476271.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.534

Publications

4 publications found

Variant links:

Genes affected

RN7SL685P (HGNC:46701): (RNA, 7SL, cytoplasmic 685, pseudogene)

RN7SL685P 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RN7SL685P		n.100957891C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RN7SL685P	ENST00000476271.3 link	n.9C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.654

AC:

99338

AN:

151806

Hom.:

33043

Cov.:

show subpopulations

Gnomad AFR

AF:

0.785

Gnomad AMI

AF:

0.581

Gnomad AMR

AF:

0.626

Gnomad ASJ

AF:

0.624

Gnomad EAS

AF:

0.609

Gnomad SAS

AF:

0.698

Gnomad FIN

AF:

0.516

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.647

GnomAD4 exome

AF:

0.656

AC:

AN:

Hom.:

Cov.:

AF XY:

0.607

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.650

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.654

AC:

99412

AN:

151924

Hom.:

33074

Cov.:

AF XY:

0.650

AC XY:

48266

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.785

AC:

32516

AN:

41430

American (AMR)

AF:

0.626

AC:

9562

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.624

AC:

2165

AN:

3472

East Asian (EAS)

AF:

0.609

AC:

3131

AN:

5144

South Asian (SAS)

AF:

0.699

AC:

3364

AN:

4812

European-Finnish (FIN)

AF:

0.516

AC:

5438

AN:

10538

Middle Eastern (MID)

AF:

0.701

AC:

206

AN:

294

European-Non Finnish (NFE)

AF:

0.606

AC:

41153

AN:

67934

Other (OTH)

AF:

0.640

AC:

1347

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1675

3350

5024

6699

8374

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

796

1592

2388

3184

3980

<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:

0.643

Hom.:

4798

Bravo

AF:

0.669

Asia WGS

AF:

0.633

AC:

2205

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.4

(source)

DANN

Benign

0.77

PhyloP100

0.53

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over