3-108256485-A-G

Variant names:

• chr3-108256485-A-G
• rs1870007

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 0.696 in 152,078 control chromosomes in the GnomAD database, including 37,087 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 0.70 (37087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105718 AN: 151960 Hom.: 37047 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.696 AC: 105810 AN: 152078 Hom.: 37087 Cov.: 32 AF XY: 0.697 AC XY: 51837 AN XY: 74354

African (AFR) AF: 0.682 AC: 28273 AN: 41430

American (AMR) AF: 0.788 AC: 12046 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2520 AN: 3468

East Asian (EAS) AF: 0.879 AC: 4564 AN: 5190

South Asian (SAS) AF: 0.730 AC: 3518 AN: 4822

European-Finnish (FIN) AF: 0.623 AC: 6591 AN: 10578

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45941 AN: 67984

Other (OTH) AF: 0.724 AC: 1533 AN: 2116

Alfa AF: 0.692 Hom.: 45201

Bravo AF: 0.707

Asia WGS AF: 0.803 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.76
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs1870007; hg19: chr3-107975332;