rs534870

chr13-80385072-G-Achr13-80385072-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;