rs10499638

Positions:

• chr7-46127333-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 0.181 in 152,106 control chromosomes in the GnomAD database, including 3,297 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 0.18 (3297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 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: 0.181 AC: 27481 AN: 151992 Hom.: 3296 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.181 AC: 27482 AN: 152106 Hom.: 3297 Cov.: 32 AF XY: 0.182 AC XY: 13567 AN XY: 74340

Gnomad4 AFR AF: 0.0473

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0170

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.162

Alfa AF: 0.232 Hom.: 1604

Bravo AF: 0.173

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499638; hg19: chr7-46166931;