rs959106

Variant names:

• chr3-108760670-A-G
• rs959106

Your query was ambiguous. Multiple possible variants found:

• chr3-108760670-A-G
• chr3-108760670-A-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 0.15 in 152,186 control chromosomes in the GnomAD database, including 1,794 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 0.15 (1794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 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: 0.150 AC: 22789 AN: 152066 Hom.: 1794 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0700

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.150 AC: 22793 AN: 152186 Hom.: 1794 Cov.: 32 AF XY: 0.146 AC XY: 10869 AN XY: 74386

African (AFR) AF: 0.106 AC: 4394 AN: 41518

American (AMR) AF: 0.139 AC: 2128 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5176

South Asian (SAS) AF: 0.0710 AC: 343 AN: 4830

European-Finnish (FIN) AF: 0.152 AC: 1608 AN: 10590

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13116 AN: 68000

Other (OTH) AF: 0.168 AC: 355 AN: 2110

Alfa AF: 0.154 Hom.: 252

Bravo AF: 0.148

Asia WGS AF: 0.0430 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.49
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs959106; hg19: chr3-108479517;