rs4942577

chr13-46823319-C-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 0.716 in 152,134 control chromosomes in the GnomAD database, including 39,979 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 0.72 (39979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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: 0.716 AC: 108840 AN: 152016 Hom.: 39941 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.716 AC: 108931 AN: 152134 Hom.: 39979 Cov.: 32 AF XY: 0.707 AC XY: 52607 AN XY: 74378

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.736

Alfa AF: 0.687 Hom.: 18894

Bravo AF: 0.740

Asia WGS AF: 0.635 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.86
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4942577; hg19: chr13-47397454;