rs534870

Variant names:

• chr13-80385072-G-A
• rs534870

Your query was ambiguous. Multiple possible variants found:

• chr13-80385072-G-A
• chr13-80385072-G-C

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 0.709 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.709 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

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.689

Alfa AF: 0.688 Hom.: 66887

Bravo AF: 0.717

Asia WGS AF: 0.614 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs534870; hg19: chr13-80959207;