dbSNP rs9691864: ENSG00000303536:n.211-12382C>T (chr7-54824378-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000795375.1(ENSG00000303536):n.211-12382C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,736 control chromosomes in the GnomAD database, including 7,583 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 0.30 ( 7583 hom., cov: 31)

Consequence

ENSG00000303536
ENST00000795375.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.789

Publications

2 publications found

Variant links:

Genes affected

ENSG00000303536 (HGNC:):

ENSG00000303536 links:

Genome browser will be placed here

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=-0.72).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000303536	ENST00000795375.1 link	n.211-12382C>T	intron_variant	Intron 2 of 3
ENSG00000303536	ENST00000795376.1 link	n.147-12382C>T	intron_variant	Intron 2 of 3
ENSG00000303536	ENST00000795377.1 link	n.274-12382C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45762

AN:

151618

Hom.:

7589

Cov.:

show subpopulations

Gnomad AFR

AF:

0.189

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.0738

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.269

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.328

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.302

AC:

45764

AN:

151736

Hom.:

7583

Cov.:

AF XY:

0.295

AC XY:

21879

AN XY:

74148

show subpopulations

African (AFR)

AF:

0.189

AC:

7805

AN:

41348

American (AMR)

AF:

0.333

AC:

5066

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.383

AC:

1327

AN:

3466

East Asian (EAS)

AF:

0.0739

AC:

381

AN:

5154

South Asian (SAS)

AF:

0.296

AC:

1416

AN:

4790

European-Finnish (FIN)

AF:

0.269

AC:

2830

AN:

10506

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.379

AC:

25735

AN:

67920

Other (OTH)

AF:

0.327

AC:

690

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1551

3101

4652

6202

7753

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.362

Hom.:

16858

Bravo

AF:

0.299

Asia WGS

AF:

0.182

AC:

632

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

4.0

(source)

DANN

Benign

0.87

PhyloP100

0.79

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over