rs10498269

Variant names:

• chr14-20549259-C-T
• rs10498269

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 0.349 in 151,776 control chromosomes in the GnomAD database, including 10,545 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 0.35 (10545 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 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: 0.350 AC: 53009 AN: 151658 Hom.: 10542 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.349 AC: 53015 AN: 151776 Hom.: 10545 Cov.: 31 AF XY: 0.347 AC XY: 25709 AN XY: 74168

African (AFR) AF: 0.167 AC: 6920 AN: 41404

American (AMR) AF: 0.295 AC: 4492 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1790 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1571 AN: 5148

South Asian (SAS) AF: 0.313 AC: 1506 AN: 4814

European-Finnish (FIN) AF: 0.435 AC: 4568 AN: 10490

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30880 AN: 67894

Other (OTH) AF: 0.384 AC: 809 AN: 2108

Alfa AF: 0.414 Hom.: 16213

Bravo AF: 0.329

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.59
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10498269; hg19: chr14-21017418;