rs10483466

Variant names:

• chr14-36447871-T-C
• rs10483466
• ENST00000634305.1:n.251-895T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000634305.1(ENSG00000283098):​n.251-895T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0561 in 152,276 control chromosomes in the GnomAD database, including 516 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 0.056 (516 hom., cov: 32)
• Consequence: ENSG00000283098 ENST00000634305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354

Genes affected

ENSG00000283098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 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
ENSG00000283098	ENST00000634305.1	n.251-895T>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0561 AC: 8537 AN: 152158 Hom.: 511 Cov.: 32

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0927

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0561 AC: 8548 AN: 152276 Hom.: 516 Cov.: 32 AF XY: 0.0626 AC XY: 4662 AN XY: 74460

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.0927

Gnomad4 NFE AF: 0.0339

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0422 Hom.: 486

Bravo AF: 0.0597

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483466; hg19: chr14-36917076;