rs340560

Variant names:

• chr13-72273956-G-A
• rs340560

Your query was ambiguous. Multiple possible variants found:

• chr13-72273956-G-A
• chr13-72273956-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;