13-85315505-A-G

Variant names:

• chr13-85315505-A-G
• rs1571830

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 0.587 in 151,668 control chromosomes in the GnomAD database, including 27,644 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 0.59 (27644 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.95
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 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: 0.587 AC: 88971 AN: 151548 Hom.: 27621 Cov.: 30

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.587 AC: 89020 AN: 151668 Hom.: 27644 Cov.: 30 AF XY: 0.595 AC XY: 44113 AN XY: 74108

African (AFR) AF: 0.383 AC: 15813 AN: 41300

American (AMR) AF: 0.699 AC: 10647 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3466

East Asian (EAS) AF: 0.834 AC: 4301 AN: 5160

South Asian (SAS) AF: 0.648 AC: 3111 AN: 4800

European-Finnish (FIN) AF: 0.762 AC: 7994 AN: 10494

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43743 AN: 67914

Other (OTH) AF: 0.578 AC: 1217 AN: 2104

Alfa AF: 0.524 Hom.: 1720

Bravo AF: 0.576

Asia WGS AF: 0.728 AC: 2533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.042
DANN	Benign	0.29
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs1571830; hg19: chr13-85889640;