rs3763313

Variant names:

• chr6-32408694-A-C
• rs3763313

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.215

Alfa AF: 0.190 Hom.: 4987

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763313; hg19: chr6-32376471;