rs10507372

Positions:

• chr13-26749470-C-A
• chr13-26749470-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0122

Gnomad4 AMR AF: 0.0512

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.000429

Gnomad4 SAS AF: 0.0280

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.0476

Alfa AF: 0.0644 Hom.: 501

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507372; hg19: chr13-27323607;