rs3763311

chr6-32408399-C-T

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/exons	MANE	UniProt

Ensembl

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