chr2-169119595-T-G

Variant names:

• chr2-169119595-T-G
• rs4668121

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 0.669 in 152,072 control chromosomes in the GnomAD database, including 34,708 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 0.67 (34708 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 8 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 (SAS) allele frequency at 95% confidence interval = 0.727 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: 0.670 AC: 101735 AN: 151954 Hom.: 34698 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.669 AC: 101782 AN: 152072 Hom.: 34708 Cov.: 32 AF XY: 0.671 AC XY: 49843 AN XY: 74328

African (AFR) AF: 0.555 AC: 23024 AN: 41452

American (AMR) AF: 0.721 AC: 11015 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2235 AN: 3472

East Asian (EAS) AF: 0.403 AC: 2084 AN: 5172

South Asian (SAS) AF: 0.746 AC: 3598 AN: 4826

European-Finnish (FIN) AF: 0.729 AC: 7713 AN: 10576

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49759 AN: 67980

Other (OTH) AF: 0.688 AC: 1451 AN: 2108

Alfa AF: 0.713 Hom.: 57651

Bravo AF: 0.658

Asia WGS AF: 0.605 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4668121; hg19: chr2-169976105;