13-85315505-A-G

Variant names:

• chr13-85315505-A-G
• rs1571830

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 0.587 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.587 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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.578

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1571830; hg19: chr13-85889640;