rs10507592

Positions:

• chr13-54507972-T-A

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 0.0629 in 152,136 control chromosomes in the GnomAD database, including 406 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 0.063 (406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 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: 0.0628 AC: 9551 AN: 152018 Hom.: 401 Cov.: 32

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0605

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0629 AC: 9563 AN: 152136 Hom.: 406 Cov.: 32 AF XY: 0.0657 AC XY: 4885 AN XY: 74366

Gnomad4 AFR AF: 0.0366

Gnomad4 AMR AF: 0.0558

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.0605

Gnomad4 NFE AF: 0.0643

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0311 Hom.: 17

Bravo AF: 0.0572

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507592; hg19: chr13-55082107;