rs7335631

Variant names:

• chr13-30383551-C-A
• rs7335631

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.842 in 152,054 control chromosomes in the GnomAD database, including 54,812 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 0.84 (54812 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127915 AN: 151936 Hom.: 54784 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.842 AC: 127994 AN: 152054 Hom.: 54812 Cov.: 31 AF XY: 0.846 AC XY: 62932 AN XY: 74344

African (AFR) AF: 0.669 AC: 27699 AN: 41402

American (AMR) AF: 0.907 AC: 13852 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3254 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5166 AN: 5180

South Asian (SAS) AF: 0.964 AC: 4645 AN: 4818

European-Finnish (FIN) AF: 0.902 AC: 9541 AN: 10574

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.896 AC: 60920 AN: 68018

Other (OTH) AF: 0.873 AC: 1846 AN: 2114

Alfa AF: 0.853 Hom.: 42091

Bravo AF: 0.833

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.0
DANN	Benign	0.80
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs7335631; hg19: chr13-30957688;