rs977405

Variant names:

• chr13-72299850-G-A
• rs977405

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 0.103 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.153 AC: 6316 AN: 41384

American (AMR) AF: 0.0867 AC: 1316 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.0694 AC: 240 AN: 3460

East Asian (EAS) AF: 0.122 AC: 625 AN: 5138

South Asian (SAS) AF: 0.0976 AC: 470 AN: 4816

European-Finnish (FIN) AF: 0.0503 AC: 532 AN: 10572

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0870 AC: 5882 AN: 67580

Other (OTH) AF: 0.0931 AC: 196 AN: 2106

Alfa AF: 0.0939 Hom.: 154

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
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs977405; hg19: chr13-72873988;