2-156896859-A-T

Variant names:

• chr2-156896859-A-T
• rs295796

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 0.743 in 151,636 control chromosomes in the GnomAD database, including 44,390 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 0.74 (44390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 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: 0.743 AC: 112561 AN: 151518 Hom.: 44366 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.743 AC: 112627 AN: 151636 Hom.: 44390 Cov.: 32 AF XY: 0.743 AC XY: 55028 AN XY: 74066

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.749

Alfa AF: 0.768 Hom.: 3022

Bravo AF: 0.726

Asia WGS AF: 0.785 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.10
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs295796; hg19: chr2-157753371;