chr13-42524211-A-G

Variant names:

• chr13-42524211-A-G
• rs4941432

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 0.711 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.711 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

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.725

Alfa AF: 0.703 Hom.: 5331

Bravo AF: 0.727

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4941432; hg19: chr13-43098347;