2-172098631-A-T

Variant names:

• chr2-172098631-A-T
• rs4519482

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.592 in 152,060 control chromosomes in the GnomAD database, including 27,783 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 0.59 (27783 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 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: 0.592 AC: 89997 AN: 151942 Hom.: 27768 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.592 AC: 90047 AN: 152060 Hom.: 27783 Cov.: 32 AF XY: 0.596 AC XY: 44297 AN XY: 74316

African (AFR) AF: 0.400 AC: 16593 AN: 41458

American (AMR) AF: 0.623 AC: 9526 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2128 AN: 3470

East Asian (EAS) AF: 0.834 AC: 4318 AN: 5180

South Asian (SAS) AF: 0.768 AC: 3709 AN: 4828

European-Finnish (FIN) AF: 0.595 AC: 6284 AN: 10556

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45404 AN: 67980

Other (OTH) AF: 0.609 AC: 1284 AN: 2110

Alfa AF: 0.616 Hom.: 3703

Bravo AF: 0.584

Asia WGS AF: 0.736 AC: 2560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.99
DANN	Benign	0.50
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4519482; hg19: chr2-172963359;