rs10492757

Variant names:

• chr16-7724637-A-C
• rs10492757

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 0.139 in 152,164 control chromosomes in the GnomAD database, including 1,668 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 0.14 (1668 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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: 0.139 AC: 21172 AN: 152046 Hom.: 1664 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.139 AC: 21213 AN: 152164 Hom.: 1668 Cov.: 32 AF XY: 0.136 AC XY: 10107 AN XY: 74402

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0954

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.00965

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0618

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.136

Alfa AF: 0.129 Hom.: 1439

Bravo AF: 0.144

Asia WGS AF: 0.0660 AC: 230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492757; hg19: chr16-7774639;