rs238358

Positions:

• chr13-42264538-A-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 0.841 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.861

Alfa AF: 0.903 Hom.: 84056

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs238358; hg19: chr13-42838674;