2-81922490-T-G

Position:

• chr2-81922490-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 0.177 in 148,162 control chromosomes in the GnomAD database, including 2,360 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 0.18 (2360 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699

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 (NFE) allele frequency at 95% confidence interval = 0.199 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: 0.177 AC: 26178 AN: 148044 Hom.: 2355 Cov.: 27

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0510

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.219

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.177 AC: 26189 AN: 148162 Hom.: 2360 Cov.: 27 AF XY: 0.174 AC XY: 12547 AN XY: 72016

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0511

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.193

Alfa AF: 0.190 Hom.: 1234

Bravo AF: 0.172

Asia WGS AF: 0.106 AC: 368 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	0.95
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: rs10520308; hg19: chr2-82149614;