rs10507344

Variant names:

• chr13-25150931-C-T
• rs10507344

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 0.136 in 152,154 control chromosomes in the GnomAD database, including 1,542 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 0.14 (1542 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 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: 0.136 AC: 20704 AN: 152038 Hom.: 1538 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.136 AC: 20720 AN: 152154 Hom.: 1542 Cov.: 32 AF XY: 0.141 AC XY: 10485 AN XY: 74364

African (AFR) AF: 0.127 AC: 5271 AN: 41532

American (AMR) AF: 0.158 AC: 2416 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1463 AN: 5156

South Asian (SAS) AF: 0.270 AC: 1303 AN: 4826

European-Finnish (FIN) AF: 0.130 AC: 1374 AN: 10588

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7791 AN: 67986

Other (OTH) AF: 0.149 AC: 313 AN: 2106

Alfa AF: 0.127 Hom.: 4375

Bravo AF: 0.138

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs10507344; hg19: chr13-25725069;