rs10498269

chr14-20549259-C-T

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 0.349 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.384

Alfa AF: 0.416 Hom.: 13598

Bravo AF: 0.329

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.2
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: rs10498269; hg19: chr14-21017418;