chr2-157090888-G-A

Variant names:

• chr2-157090888-G-A
• rs13401572

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 0.162 in 152,032 control chromosomes in the GnomAD database, including 3,044 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 0.16 (3044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 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: 0.162 AC: 24579 AN: 151914 Hom.: 3034 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0815

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.162 AC: 24619 AN: 152032 Hom.: 3044 Cov.: 32 AF XY: 0.162 AC XY: 12046 AN XY: 74302

African (AFR) AF: 0.343 AC: 14217 AN: 41444

American (AMR) AF: 0.116 AC: 1776 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3472

East Asian (EAS) AF: 0.122 AC: 631 AN: 5170

South Asian (SAS) AF: 0.0298 AC: 144 AN: 4828

European-Finnish (FIN) AF: 0.154 AC: 1622 AN: 10564

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0795 AC: 5405 AN: 67976

Other (OTH) AF: 0.155 AC: 326 AN: 2110

Alfa AF: 0.0885 Hom.: 1259

Bravo AF: 0.170

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.018
DANN	Benign	0.19
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs13401572; hg19: chr2-157947400;