rs3763313

Variant names:

• chr6-32408694-A-C
• rs3763313

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 0.207 in 152,176 control chromosomes in the GnomAD database, including 3,397 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 0.21 (3397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 81 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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: 0.207 AC: 31447 AN: 152058 Hom.: 3393 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.207 AC: 31472 AN: 152176 Hom.: 3397 Cov.: 32 AF XY: 0.212 AC XY: 15755 AN XY: 74394

African (AFR) AF: 0.207 AC: 8592 AN: 41512

American (AMR) AF: 0.205 AC: 3126 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1043 AN: 5180

South Asian (SAS) AF: 0.156 AC: 753 AN: 4830

European-Finnish (FIN) AF: 0.322 AC: 3412 AN: 10582

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13010 AN: 68002

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.190 Hom.: 11429

Bravo AF: 0.200

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.57
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs3763313; hg19: chr6-32376471;