rs10492693

Positions:

• chr13-38951505-T-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 0.0539 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;