chr2-173462117-C-T

Position:

• chr2-173462117-C-T

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 0.139 in 152,026 control chromosomes in the GnomAD database, including 1,847 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 0.14 (1847 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 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: 0.139 AC: 21091 AN: 151908 Hom.: 1850 Cov.: 32

Gnomad AFR AF: 0.0381

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0317

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.139 AC: 21087 AN: 152026 Hom.: 1847 Cov.: 32 AF XY: 0.139 AC XY: 10303 AN XY: 74290

Gnomad4 AFR AF: 0.0380

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.147

Alfa AF: 0.176 Hom.: 602

Bravo AF: 0.125

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10930597; hg19: chr2-174326845;