chr3-171498966-G-A

Variant names:

• chr3-171498966-G-A
• rs10490809

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 0.77 in 151,986 control chromosomes in the GnomAD database, including 45,096 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 0.77 (45096 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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: 0.770 AC: 116877 AN: 151868 Hom.: 45047 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.770 AC: 116987 AN: 151986 Hom.: 45096 Cov.: 31 AF XY: 0.766 AC XY: 56895 AN XY: 74286

African (AFR) AF: 0.796 AC: 32965 AN: 41438

American (AMR) AF: 0.752 AC: 11491 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2873 AN: 3472

East Asian (EAS) AF: 0.742 AC: 3836 AN: 5170

South Asian (SAS) AF: 0.750 AC: 3614 AN: 4816

European-Finnish (FIN) AF: 0.720 AC: 7588 AN: 10536

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52032 AN: 67968

Other (OTH) AF: 0.786 AC: 1659 AN: 2112

Alfa AF: 0.762 Hom.: 6851

Bravo AF: 0.777

Asia WGS AF: 0.769 AC: 2672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.45
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs10490809; hg19: chr3-171216755;