rs10498750

Variant names:

• chr6-40649151-T-C
• rs10498750

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;