rs3763312

Variant names:

• chr6-32408571-G-A
• rs3763312

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 152,118 control chromosomes in the GnomAD database, including 2,499 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 (2499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 44 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 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: 26537 AN: 152000 Hom.: 2499 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.175 AC: 26546 AN: 152118 Hom.: 2499 Cov.: 32 AF XY: 0.174 AC XY: 12921 AN XY: 74352

African (AFR) AF: 0.104 AC: 4307 AN: 41490

American (AMR) AF: 0.207 AC: 3172 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3468

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

South Asian (SAS) AF: 0.202 AC: 974 AN: 4816

European-Finnish (FIN) AF: 0.180 AC: 1898 AN: 10568

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14289 AN: 67982

Other (OTH) AF: 0.153 AC: 324 AN: 2114

Alfa AF: 0.209 Hom.: 9531

Bravo AF: 0.179

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.25
DANN	Benign	0.73
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs3763312; hg19: chr6-32376348;