chr2-169119595-T-G

Position:

• chr2-169119595-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.688

Alfa AF: 0.716 Hom.: 38815

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4668121; hg19: chr2-169976105;