6-47351082-G-A

Variant names:

• chr6-47351082-G-A
• rs3905310

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 0.102 in 152,112 control chromosomes in the GnomAD database, including 1,849 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 0.10 (1849 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 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: 0.101 AC: 15407 AN: 151994 Hom.: 1836 Cov.: 32

Gnomad AFR AF: 0.0945

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.102 AC: 15456 AN: 152112 Hom.: 1849 Cov.: 32 AF XY: 0.108 AC XY: 8021 AN XY: 74374

African (AFR) AF: 0.0948 AC: 3936 AN: 41516

American (AMR) AF: 0.240 AC: 3667 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0602 AC: 209 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3048 AN: 5142

South Asian (SAS) AF: 0.145 AC: 699 AN: 4816

European-Finnish (FIN) AF: 0.0554 AC: 588 AN: 10608

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0454 AC: 3084 AN: 67984

Other (OTH) AF: 0.0985 AC: 207 AN: 2102

Alfa AF: 0.0673 Hom.: 182

Bravo AF: 0.120

Asia WGS AF: 0.340 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs3905310; hg19: chr6-47318818;