rs10492757

Positions:

• chr16-7724637-A-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;