chr13-42264538-A-G

Variant names:

• chr13-42264538-A-G
• rs238358

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 0.841 in 152,204 control chromosomes in the GnomAD database, including 54,854 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 0.84 (54854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.842 AC: 128012 AN: 152086 Hom.: 54840 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.841 AC: 128074 AN: 152204 Hom.: 54854 Cov.: 32 AF XY: 0.843 AC XY: 62730 AN XY: 74412

African (AFR) AF: 0.662 AC: 27451 AN: 41490

American (AMR) AF: 0.922 AC: 14093 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3299 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5173 AN: 5190

South Asian (SAS) AF: 0.937 AC: 4521 AN: 4826

European-Finnish (FIN) AF: 0.853 AC: 9040 AN: 10602

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61653 AN: 68022

Other (OTH) AF: 0.861 AC: 1820 AN: 2114

Alfa AF: 0.895 Hom.: 104731

Bravo AF: 0.837

Asia WGS AF: 0.948 AC: 3293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.33
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs238358; hg19: chr13-42838674;