rs3763313

chr6-32408694-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;