rs10507592

Variant names:

• chr13-54507972-T-A
• rs10507592

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0366 AC: 1521 AN: 41518

American (AMR) AF: 0.0558 AC: 853 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3470

East Asian (EAS) AF: 0.108 AC: 557 AN: 5162

South Asian (SAS) AF: 0.220 AC: 1059 AN: 4818

European-Finnish (FIN) AF: 0.0605 AC: 641 AN: 10592

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0643 AC: 4371 AN: 67974

Other (OTH) AF: 0.0766 AC: 162 AN: 2114

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
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10507592; hg19: chr13-55082107;