rs10498306

Variant names:

• chr14-29475997-T-C
• rs10498306
• ENST00000652296.1:n.127+24337A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652296.1(ENSG00000286040):​n.127+24337A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,094 control chromosomes in the GnomAD database, including 1,504 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 0.13 (1504 hom., cov: 32)
• Consequence: ENSG00000286040 ENST00000652296.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

ENSG00000286040 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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
ENSG00000286040	ENST00000652296.1	n.127+24337A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19714 AN: 151976 Hom.: 1499 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.130 AC: 19746 AN: 152094 Hom.: 1504 Cov.: 32 AF XY: 0.131 AC XY: 9722 AN XY: 74362

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.137

Alfa AF: 0.127 Hom.: 1746

Bravo AF: 0.126

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498306; hg19: chr14-29945203;