rs4942577

Variant names:

• chr13-46823319-C-T
• rs4942577

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;