rs10492693

Variant names:

• chr13-38951505-T-G
• rs10492693

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 0.0539 in 152,280 control chromosomes in the GnomAD database, including 371 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 0.054 (371 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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: 0.0538 AC: 8183 AN: 152162 Hom.: 364 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0539 AC: 8215 AN: 152280 Hom.: 371 Cov.: 33 AF XY: 0.0517 AC XY: 3847 AN XY: 74464

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0729

Gnomad4 EAS AF: 0.00250

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.0227

Gnomad4 NFE AF: 0.0273

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0415 Hom.: 23

Bravo AF: 0.0582

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.091
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492693; hg19: chr13-39525642;