rs10498807

Positions:

• chr6-55902078-A-G

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 0.182 in 152,166 control chromosomes in the GnomAD database, including 3,447 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 0.18 (3447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

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 (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27720 AN: 152048 Hom.: 3447 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.182 AC: 27747 AN: 152166 Hom.: 3447 Cov.: 32 AF XY: 0.179 AC XY: 13299 AN XY: 74406

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0997

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.166

Alfa AF: 0.156 Hom.: 394

Bravo AF: 0.195

Asia WGS AF: 0.129 AC: 448 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498807; hg19: chr6-55766876;