chr13-107118887-C-T

Variant names:

• chr13-107118887-C-T
• rs9634463

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 0.268 in 151,992 control chromosomes in the GnomAD database, including 5,705 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 0.27 (5705 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.268 AC: 40725 AN: 151872 Hom.: 5709 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.268 AC: 40742 AN: 151992 Hom.: 5705 Cov.: 32 AF XY: 0.271 AC XY: 20167 AN XY: 74308

African (AFR) AF: 0.329 AC: 13624 AN: 41428

American (AMR) AF: 0.205 AC: 3126 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2068 AN: 5160

South Asian (SAS) AF: 0.330 AC: 1582 AN: 4798

European-Finnish (FIN) AF: 0.301 AC: 3181 AN: 10568

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15618 AN: 67982

Other (OTH) AF: 0.236 AC: 499 AN: 2114

Alfa AF: 0.253 Hom.: 624

Bravo AF: 0.261

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.1
DANN	Benign	0.65
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs9634463; hg19: chr13-107771235;