13-80385072-G-A

Variant names:

• chr13-80385072-G-A
• rs534870

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 0.709 in 152,036 control chromosomes in the GnomAD database, including 38,557 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 (38557 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107746 AN: 151916 Hom.: 38516 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.709 AC: 107849 AN: 152036 Hom.: 38557 Cov.: 31 AF XY: 0.707 AC XY: 52532 AN XY: 74316

African (AFR) AF: 0.786 AC: 32622 AN: 41478

American (AMR) AF: 0.710 AC: 10832 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3472

East Asian (EAS) AF: 0.574 AC: 2952 AN: 5142

South Asian (SAS) AF: 0.569 AC: 2738 AN: 4812

European-Finnish (FIN) AF: 0.717 AC: 7575 AN: 10564

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46621 AN: 67992

Other (OTH) AF: 0.689 AC: 1452 AN: 2106

Alfa AF: 0.693 Hom.: 144054

Bravo AF: 0.717

Asia WGS AF: 0.614 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.46
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs534870; hg19: chr13-80959207;