rs1361540

Variant names:

• chr13-78923760-G-A
• rs1361540

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.811 in 152,142 control chromosomes in the GnomAD database, including 50,138 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 0.81 (50138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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: 0.811 AC: 123239 AN: 152024 Hom.: 50103 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.811 AC: 123329 AN: 152142 Hom.: 50138 Cov.: 32 AF XY: 0.812 AC XY: 60436 AN XY: 74402

African (AFR) AF: 0.777 AC: 32244 AN: 41486

American (AMR) AF: 0.886 AC: 13543 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2856 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4860 AN: 5184

South Asian (SAS) AF: 0.869 AC: 4190 AN: 4824

European-Finnish (FIN) AF: 0.794 AC: 8401 AN: 10586

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54611 AN: 67990

Other (OTH) AF: 0.822 AC: 1738 AN: 2114

Alfa AF: 0.810 Hom.: 147874

Bravo AF: 0.816

Asia WGS AF: 0.893 AC: 3104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.049
DANN	Benign	0.34
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1361540; hg19: chr13-79497895;