rs10499653

chr7-47106226-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 0.0951 in 152,254 control chromosomes in the GnomAD database, including 873 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 0.095 (873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

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 (NFE) allele frequency at 95% confidence interval = 0.133 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: 0.0952 AC: 14485 AN: 152136 Hom.: 873 Cov.: 32

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.0951 AC: 14485 AN: 152254 Hom.: 873 Cov.: 32 AF XY: 0.0928 AC XY: 6908 AN XY: 74438

Gnomad4 AFR AF: 0.0239

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.125

Alfa AF: 0.133 Hom.: 1967

Bravo AF: 0.0927

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.6
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499653; hg19: chr7-47145824;