rs10498883

Variant names:

• chr6-72441923-C-T
• rs10498883

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 0.209 in 151,980 control chromosomes in the GnomAD database, including 3,562 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 0.21 (3562 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 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: 0.209 AC: 31784 AN: 151862 Hom.: 3557 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.209 AC: 31810 AN: 151980 Hom.: 3562 Cov.: 33 AF XY: 0.208 AC XY: 15451 AN XY: 74282

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.206

Alfa AF: 0.207 Hom.: 1281

Bravo AF: 0.228

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498883; hg19: chr6-73151625;