rs10507451

Variant names:

• chr13-37303389-T-A
• rs10507451

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 0.031 in 152,318 control chromosomes in the GnomAD database, including 173 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 0.031 (173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 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: 0.0310 AC: 4715 AN: 152200 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0173

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0114

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.00401

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0310 AC: 4727 AN: 152318 Hom.: 173 Cov.: 32 AF XY: 0.0311 AC XY: 2317 AN XY: 74482

Gnomad4 AFR AF: 0.0793

Gnomad4 AMR AF: 0.0172

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.0612

Gnomad4 SAS AF: 0.0595

Gnomad4 FIN AF: 0.0114

Gnomad4 NFE AF: 0.00401

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.0202 Hom.: 17

Bravo AF: 0.0319

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507451; hg19: chr13-37877526;