rs3763311

Variant names:

• chr6-32408399-C-T
• rs3763311

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 0.285 in 151,914 control chromosomes in the GnomAD database, including 6,279 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 0.29 (6279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 38 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43277 AN: 151796 Hom.: 6277 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.285 AC: 43304 AN: 151914 Hom.: 6279 Cov.: 32 AF XY: 0.284 AC XY: 21060 AN XY: 74236

African (AFR) AF: 0.275 AC: 11393 AN: 41368

American (AMR) AF: 0.314 AC: 4799 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1157 AN: 3464

East Asian (EAS) AF: 0.342 AC: 1768 AN: 5170

South Asian (SAS) AF: 0.344 AC: 1659 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2258 AN: 10556

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19409 AN: 67956

Other (OTH) AF: 0.272 AC: 575 AN: 2114

Alfa AF: 0.292 Hom.: 24387

Bravo AF: 0.298

Asia WGS AF: 0.334 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.68
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs3763311; hg19: chr6-32376176;