rs10499658

Positions:

• chr7-47183968-G-A

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 152,094 control chromosomes in the GnomAD database, including 1,473 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 (1473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.207 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: 0.140 AC: 21204 AN: 151978 Hom.: 1473 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.139 AC: 21207 AN: 152094 Hom.: 1473 Cov.: 32 AF XY: 0.141 AC XY: 10445 AN XY: 74338

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.138

Alfa AF: 0.136 Hom.: 206

Bravo AF: 0.133

Asia WGS AF: 0.177 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499658; hg19: chr7-47223566;