rs10498807

Variant names:

• chr6-55902078-A-G
• rs10498807

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 0.182 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
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.339 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: 0.182 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

African (AFR) AF: 0.343 AC: 14255 AN: 41504

American (AMR) AF: 0.185 AC: 2832 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3472

East Asian (EAS) AF: 0.0997 AC: 516 AN: 5178

South Asian (SAS) AF: 0.128 AC: 619 AN: 4830

European-Finnish (FIN) AF: 0.101 AC: 1068 AN: 10612

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7300 AN: 67978

Other (OTH) AF: 0.166 AC: 350 AN: 2110

Alfa AF: 0.161 Hom.: 432

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10498807; hg19: chr6-55766876;