rs3763309

Variant names:

• chr6-32408196-C-A
• rs3763309

Your query was ambiguous. Multiple possible variants found:

• chr6-32408196-C-A
• chr6-32408196-C-G
• chr6-32408196-C-T

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 0.175 in 152,098 control chromosomes in the GnomAD database, including 2,510 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 0.17 (2510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 53 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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: 0.175 AC: 26572 AN: 151980 Hom.: 2510 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.175 AC: 26581 AN: 152098 Hom.: 2510 Cov.: 32 AF XY: 0.174 AC XY: 12955 AN XY: 74348

African (AFR) AF: 0.104 AC: 4309 AN: 41480

American (AMR) AF: 0.207 AC: 3169 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3472

East Asian (EAS) AF: 0.103 AC: 535 AN: 5180

South Asian (SAS) AF: 0.203 AC: 981 AN: 4822

European-Finnish (FIN) AF: 0.180 AC: 1905 AN: 10560

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14309 AN: 67984

Other (OTH) AF: 0.153 AC: 323 AN: 2114

Alfa AF: 0.198 Hom.: 8792

Bravo AF: 0.179

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.22
DANN	Benign	0.43
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs3763309; hg19: chr6-32375973;