rs10492756

Variant names:

• chr16-7753015-C-T
• rs10492756

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 0.119 in 114,878 control chromosomes in the GnomAD database, including 635 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 0.12 (635 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 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: 0.119 AC: 13677 AN: 114786 Hom.: 634 Cov.: 30

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0583

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.00873

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.110

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.119 AC: 13704 AN: 114878 Hom.: 635 Cov.: 30 AF XY: 0.119 AC XY: 6652 AN XY: 55666

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.0812

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.00875

Gnomad4 SAS AF: 0.0869

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.101

Alfa AF: 0.100 Hom.: 586

Bravo AF: 0.0838

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.74
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492756; hg19: chr16-7803017;