rs10498818

Positions:

• chr6-62366265-G-T

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 0.134 in 151,948 control chromosomes in the GnomAD database, including 1,771 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 0.13 (1771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407

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 (NFE) allele frequency at 95% confidence interval = 0.18 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: 0.134 AC: 20348 AN: 151830 Hom.: 1774 Cov.: 32

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.0844

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.134 AC: 20345 AN: 151948 Hom.: 1771 Cov.: 32 AF XY: 0.137 AC XY: 10146 AN XY: 74262

Gnomad4 AFR AF: 0.0331

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0715

Gnomad4 EAS AF: 0.0844

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.121

Alfa AF: 0.160 Hom.: 355

Bravo AF: 0.117

Asia WGS AF: 0.107 AC: 373 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498818; hg19: chr6-63076170;