rs10498069

Variant names:

• chr2-219795980-G-A
• rs10498069

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 0.219 in 152,056 control chromosomes in the GnomAD database, including 3,738 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 0.22 (3738 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.219 AC: 33327 AN: 151938 Hom.: 3732 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.219 AC: 33368 AN: 152056 Hom.: 3738 Cov.: 32 AF XY: 0.221 AC XY: 16438 AN XY: 74314

African (AFR) AF: 0.228 AC: 9473 AN: 41464

American (AMR) AF: 0.263 AC: 4013 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1624 AN: 5158

South Asian (SAS) AF: 0.147 AC: 705 AN: 4810

European-Finnish (FIN) AF: 0.226 AC: 2390 AN: 10554

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13805 AN: 68004

Other (OTH) AF: 0.223 AC: 471 AN: 2112

Alfa AF: 0.210 Hom.: 582

Bravo AF: 0.224

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	15
DANN	Benign	0.77
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs10498069; hg19: chr2-220660702;