rs10498851

Variant names:

• chr6-67254871-G-A
• rs10498851

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 0.372 in 151,864 control chromosomes in the GnomAD database, including 11,677 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 0.37 (11677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56407 AN: 151744 Hom.: 11671 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.372 AC: 56424 AN: 151864 Hom.: 11677 Cov.: 32 AF XY: 0.370 AC XY: 27484 AN XY: 74208

African (AFR) AF: 0.182 AC: 7557 AN: 41424

American (AMR) AF: 0.412 AC: 6286 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3466

East Asian (EAS) AF: 0.281 AC: 1452 AN: 5162

South Asian (SAS) AF: 0.319 AC: 1532 AN: 4806

European-Finnish (FIN) AF: 0.467 AC: 4926 AN: 10548

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31941 AN: 67906

Other (OTH) AF: 0.382 AC: 805 AN: 2106

Alfa AF: 0.447 Hom.: 23955

Bravo AF: 0.365

Asia WGS AF: 0.289 AC: 1003 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.39
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10498851; hg19: chr6-67964764;