13-108016199-T-C

Variant names:

• chr13-108016199-T-C
• rs12871532

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 0.461 in 151,994 control chromosomes in the GnomAD database, including 17,050 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 0.46 (17050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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: 0.461 AC: 70020 AN: 151876 Hom.: 17050 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.461 AC: 70023 AN: 151994 Hom.: 17050 Cov.: 32 AF XY: 0.460 AC XY: 34186 AN XY: 74268

African (AFR) AF: 0.292 AC: 12108 AN: 41458

American (AMR) AF: 0.538 AC: 8214 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3446 AN: 5170

South Asian (SAS) AF: 0.511 AC: 2469 AN: 4832

European-Finnish (FIN) AF: 0.467 AC: 4933 AN: 10558

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35530 AN: 67942

Other (OTH) AF: 0.493 AC: 1037 AN: 2104

Alfa AF: 0.509 Hom.: 86291

Bravo AF: 0.460

Asia WGS AF: 0.554 AC: 1922 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34
DANN	Benign	0.37
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs12871532; hg19: chr13-108668547;