rs10507372

Variant names:

• chr13-26749470-C-A
• rs10507372

Your query was ambiguous. Multiple possible variants found:

• 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 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

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;