rs10507514

chr13-42660678-A-G

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 0.3 in 152,136 control chromosomes in the GnomAD database, including 7,080 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 0.30 (7080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 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: 0.300 AC: 45612 AN: 152018 Hom.: 7065 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.300 AC: 45663 AN: 152136 Hom.: 7080 Cov.: 33 AF XY: 0.297 AC XY: 22090 AN XY: 74364

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.269

Alfa AF: 0.308 Hom.: 1861

Bravo AF: 0.295

Asia WGS AF: 0.325 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	11
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507514; hg19: chr13-43234814;