rs10483466

chr14-36447871-T-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, non coding transcript 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: ENST00000634305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634305.1	n.251-895T>C		intron_variant, non_coding_transcript_variant		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;