rs13401572

chr2-157090888-G-Achr2-157090888-G-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 0.162 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.0795

Gnomad4 OTH AF: 0.155

Alfa AF: 0.0850 Hom.: 957

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13401572; hg19: chr2-157947400;