rs977405

Variant names:

• chr13-72299850-G-A
• rs977405

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 0.103 in 151,432 control chromosomes in the GnomAD database, including 901 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 0.10 (901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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: 0.103 AC: 15631 AN: 151312 Hom.: 894 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0694

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.0940

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

GnomAD4 genome AF: 0.103 AC: 15670 AN: 151432 Hom.: 901 Cov.: 32 AF XY: 0.102 AC XY: 7535 AN XY: 73990

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0867

Gnomad4 ASJ AF: 0.0694

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.0931

Alfa AF: 0.0922 Hom.: 149

Bravo AF: 0.108

Asia WGS AF: 0.0930 AC: 322 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	6.8
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977405; hg19: chr13-72873988;