rs10498750

Variant names:

• chr6-40649151-T-C
• rs10498750

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.151 AC: 6280 AN: 41548

American (AMR) AF: 0.194 AC: 2966 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 900 AN: 3470

East Asian (EAS) AF: 0.102 AC: 529 AN: 5178

South Asian (SAS) AF: 0.163 AC: 784 AN: 4822

European-Finnish (FIN) AF: 0.389 AC: 4122 AN: 10584

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21814 AN: 68000

Other (OTH) AF: 0.211 AC: 446 AN: 2112

Alfa AF: 0.289 Hom.: 28397

Bravo AF: 0.234

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.033
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10498750; hg19: chr6-40616890;