13-76188416-C-T

Variant names:

• chr13-76188416-C-T
• rs2810449

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 0.777 in 150,848 control chromosomes in the GnomAD database, including 46,267 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 0.78 (46267 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 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: 0.777 AC: 117144 AN: 150768 Hom.: 46254 Cov.: 28

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.777 AC: 117201 AN: 150848 Hom.: 46267 Cov.: 28 AF XY: 0.769 AC XY: 56642 AN XY: 73704

African (AFR) AF: 0.731 AC: 30080 AN: 41174

American (AMR) AF: 0.762 AC: 11525 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2425 AN: 3462

East Asian (EAS) AF: 0.430 AC: 2186 AN: 5082

South Asian (SAS) AF: 0.550 AC: 2613 AN: 4754

European-Finnish (FIN) AF: 0.842 AC: 8582 AN: 10198

Middle Eastern (MID) AF: 0.656 AC: 185 AN: 282

European-Non Finnish (NFE) AF: 0.847 AC: 57399 AN: 67766

Other (OTH) AF: 0.769 AC: 1611 AN: 2094

Alfa AF: 0.820 Hom.: 85282

Bravo AF: 0.773

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.60
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs2810449; hg19: chr13-76762552; COSMIC: COSV64441588;