rs3763311

Variant names:

• chr6-32408399-C-T
• rs3763311

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 0.285 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.285 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

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.272

Alfa AF: 0.289 Hom.: 8246

Bravo AF: 0.298

Asia WGS AF: 0.334 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763311; hg19: chr6-32376176;