chr2-162996953-T-G

Position:

• chr2-162996953-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 0.173 in 152,144 control chromosomes in the GnomAD database, including 2,805 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 0.17 (2805 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366

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 = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26287 AN: 152028 Hom.: 2805 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0891

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.173 AC: 26274 AN: 152144 Hom.: 2805 Cov.: 32 AF XY: 0.174 AC XY: 12912 AN XY: 74366

Gnomad4 AFR AF: 0.0487

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0888

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.188

Alfa AF: 0.203 Hom.: 417

Bravo AF: 0.164

Asia WGS AF: 0.103 AC: 356 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	5.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1834226; hg19: chr2-163853463;