chr13-108122814-T-C

Variant names:

• chr13-108122814-T-C
• rs1223978

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 0.524 in 151,768 control chromosomes in the GnomAD database, including 21,047 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 0.52 (21047 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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: 0.524 AC: 79423 AN: 151650 Hom.: 21015 Cov.: 30

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.524 AC: 79520 AN: 151768 Hom.: 21047 Cov.: 30 AF XY: 0.523 AC XY: 38803 AN XY: 74140

African (AFR) AF: 0.480 AC: 19842 AN: 41352

American (AMR) AF: 0.535 AC: 8170 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1697 AN: 3470

East Asian (EAS) AF: 0.696 AC: 3569 AN: 5128

South Asian (SAS) AF: 0.460 AC: 2203 AN: 4788

European-Finnish (FIN) AF: 0.518 AC: 5454 AN: 10532

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36713 AN: 67924

Other (OTH) AF: 0.524 AC: 1105 AN: 2110

Alfa AF: 0.529 Hom.: 12175

Bravo AF: 0.528

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.48
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1223978; hg19: chr13-108775162;