rs10498750

chr6-40649151-T-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 0.251 in 152,216 control chromosomes in the GnomAD database, including 5,378 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 0.25 (5378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 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: 0.252 AC: 38277 AN: 152098 Hom.: 5377 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.251 AC: 38282 AN: 152216 Hom.: 5378 Cov.: 32 AF XY: 0.249 AC XY: 18517 AN XY: 74414

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.211

Alfa AF: 0.294 Hom.: 14275

Bravo AF: 0.234

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.033
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498750; hg19: chr6-40616890;