rs340560

chr13-72273956-G-Achr13-72273956-G-T

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 0.106 in 126,802 control chromosomes in the GnomAD database, including 1,582 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 0.11 (1582 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.106 AC: 13386 AN: 126716 Hom.: 1573 Cov.: 24

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.0586

Gnomad SAS AF: 0.0434

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.106 AC: 13411 AN: 126802 Hom.: 1582 Cov.: 24 AF XY: 0.102 AC XY: 6303 AN XY: 61802

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0746

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.0590

Gnomad4 SAS AF: 0.0432

Gnomad4 FIN AF: 0.0197

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.105

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.0
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs340560; hg19: chr13-72848094;