chr13-36166285-T-C

Variant names:

• chr13-36166285-T-C
• rs12861843

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 0.434 in 152,002 control chromosomes in the GnomAD database, including 14,397 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 0.43 (14397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.52 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: 0.434 AC: 65895 AN: 151884 Hom.: 14390 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.434 AC: 65911 AN: 152002 Hom.: 14397 Cov.: 32 AF XY: 0.438 AC XY: 32524 AN XY: 74308

African (AFR) AF: 0.404 AC: 16767 AN: 41452

American (AMR) AF: 0.407 AC: 6213 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3468

East Asian (EAS) AF: 0.396 AC: 2042 AN: 5160

South Asian (SAS) AF: 0.537 AC: 2587 AN: 4818

European-Finnish (FIN) AF: 0.514 AC: 5422 AN: 10558

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29783 AN: 67956

Other (OTH) AF: 0.441 AC: 929 AN: 2108

Alfa AF: 0.442 Hom.: 25053

Bravo AF: 0.425

Asia WGS AF: 0.457 AC: 1594 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	0.17
DANN	Benign	0.42
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs12861843; hg19: chr13-36740422;