rs3763316

Variant names:

• chr6-32408969-C-T
• rs3763316

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 0.239 in 152,076 control chromosomes in the GnomAD database, including 4,590 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 0.24 (4590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.288 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: 0.240 AC: 36408 AN: 151958 Hom.: 4591 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.239 AC: 36422 AN: 152076 Hom.: 4590 Cov.: 32 AF XY: 0.236 AC XY: 17510 AN XY: 74332

African (AFR) AF: 0.182 AC: 7567 AN: 41466

American (AMR) AF: 0.295 AC: 4507 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3468

East Asian (EAS) AF: 0.148 AC: 768 AN: 5180

South Asian (SAS) AF: 0.231 AC: 1115 AN: 4824

European-Finnish (FIN) AF: 0.186 AC: 1965 AN: 10564

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.275 AC: 18665 AN: 67974

Other (OTH) AF: 0.231 AC: 486 AN: 2106

Alfa AF: 0.261 Hom.: 12833

Bravo AF: 0.253

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs3763316; hg19: chr6-32376746;