chr13-42524211-A-G

Variant names:

• chr13-42524211-A-G
• rs4941432

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 0.711 in 152,158 control chromosomes in the GnomAD database, including 38,740 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 0.71 (38740 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108155 AN: 152040 Hom.: 38715 Cov.: 34

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.711 AC: 108221 AN: 152158 Hom.: 38740 Cov.: 34 AF XY: 0.707 AC XY: 52613 AN XY: 74392

African (AFR) AF: 0.666 AC: 27636 AN: 41482

American (AMR) AF: 0.800 AC: 12235 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2491 AN: 3472

East Asian (EAS) AF: 0.780 AC: 4048 AN: 5188

South Asian (SAS) AF: 0.695 AC: 3356 AN: 4826

European-Finnish (FIN) AF: 0.631 AC: 6681 AN: 10586

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49379 AN: 67996

Other (OTH) AF: 0.725 AC: 1531 AN: 2112

Alfa AF: 0.716 Hom.: 11961

Bravo AF: 0.727

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.81
DANN	Benign	0.51
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs4941432; hg19: chr13-43098347;