chr13-26749470-C-A

Variant names:

• chr13-26749470-C-A
• rs10507372

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 0.0528 in 144,296 control chromosomes in the GnomAD database, including 280 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 0.053 (280 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.073 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: 0.0529 AC: 7628 AN: 144200 Hom.: 280 Cov.: 29

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.000428

Gnomad SAS AF: 0.0277

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.0455

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0528 AC: 7626 AN: 144296 Hom.: 280 Cov.: 29 AF XY: 0.0534 AC XY: 3713 AN XY: 69490

African (AFR) AF: 0.0122 AC: 479 AN: 39228

American (AMR) AF: 0.0512 AC: 688 AN: 13430

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 167 AN: 3430

East Asian (EAS) AF: 0.000429 AC: 2 AN: 4658

South Asian (SAS) AF: 0.0280 AC: 126 AN: 4506

European-Finnish (FIN) AF: 0.0985 AC: 891 AN: 9048

Middle Eastern (MID) AF: 0.0444 AC: 11 AN: 248

European-Non Finnish (NFE) AF: 0.0748 AC: 4998 AN: 66848

Other (OTH) AF: 0.0476 AC: 95 AN: 1996

Alfa AF: 0.0624 Hom.: 614

Bravo AF: 0.0459

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.81
DANN	Benign	0.80
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10507372; hg19: chr13-27323607;