rs13361160

Variant names:

• chr5-10169711-T-C
• rs13361160

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 0.344 in 152,048 control chromosomes in the GnomAD database, including 10,105 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 0.34 (10105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.434 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: 0.344 AC: 52324 AN: 151932 Hom.: 10105 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.344 AC: 52347 AN: 152048 Hom.: 10105 Cov.: 32 AF XY: 0.342 AC XY: 25442 AN XY: 74296

African (AFR) AF: 0.168 AC: 6962 AN: 41494

American (AMR) AF: 0.443 AC: 6771 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1514 AN: 3472

East Asian (EAS) AF: 0.136 AC: 704 AN: 5162

South Asian (SAS) AF: 0.358 AC: 1723 AN: 4818

European-Finnish (FIN) AF: 0.402 AC: 4231 AN: 10528

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29116 AN: 67980

Other (OTH) AF: 0.355 AC: 748 AN: 2106

Alfa AF: 0.382 Hom.: 19221

Bravo AF: 0.343

Asia WGS AF: 0.225 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.068
DANN	Benign	0.37
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs13361160; hg19: chr5-10169823;