rs1359536

Variant names:

• chr13-78701658-A-G
• rs1359536

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 0.0859 in 152,268 control chromosomes in the GnomAD database, including 576 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 0.086 (576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.111 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: 0.0860 AC: 13083 AN: 152150 Hom.: 577 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.0859 AC: 13081 AN: 152268 Hom.: 576 Cov.: 32 AF XY: 0.0837 AC XY: 6231 AN XY: 74456

African (AFR) AF: 0.0759 AC: 3153 AN: 41540

American (AMR) AF: 0.116 AC: 1767 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3472

East Asian (EAS) AF: 0.0901 AC: 466 AN: 5174

South Asian (SAS) AF: 0.0608 AC: 294 AN: 4832

European-Finnish (FIN) AF: 0.0493 AC: 523 AN: 10616

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0898 AC: 6109 AN: 68016

Other (OTH) AF: 0.0931 AC: 197 AN: 2116

Alfa AF: 0.0935 Hom.: 894

Bravo AF: 0.0927

Asia WGS AF: 0.0690 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.61
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1359536; hg19: chr13-79275793;