rs10498818

Variant names:

• chr6-62366265-G-T
• rs10498818

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 0.134 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0331 AC: 1373 AN: 41484

American (AMR) AF: 0.124 AC: 1892 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.0844 AC: 437 AN: 5176

South Asian (SAS) AF: 0.152 AC: 731 AN: 4822

European-Finnish (FIN) AF: 0.263 AC: 2764 AN: 10518

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12424 AN: 67894

Other (OTH) AF: 0.121 AC: 255 AN: 2116

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
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10498818; hg19: chr6-63076170;