rs10483468

Variant names:

• chr14-36454098-T-C
• rs10483468
• ENST00000634305.1:n.322+5261T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634305.1(ENSG00000283098):​n.322+5261T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0537 in 152,260 control chromosomes in the GnomAD database, including 505 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 0.054 (505 hom., cov: 32)
• Consequence: ENSG00000283098 ENST00000634305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 0 publications found

Genes affected

ENSG00000283098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 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.322+5261T>C		intron_variant	Intron 3 of 3	5
ENSG00000283098	ENST00000716789.1	n.478+5261T>C		intron_variant	Intron 4 of 5
ENSG00000283098	ENST00000716791.1	n.346-35683T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0536 AC: 8162 AN: 152142 Hom.: 501 Cov.: 32

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.0458

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

GnomAD4 genome AF: 0.0537 AC: 8170 AN: 152260 Hom.: 505 Cov.: 32 AF XY: 0.0603 AC XY: 4489 AN XY: 74442

African (AFR) AF: 0.0221 AC: 917 AN: 41560

American (AMR) AF: 0.128 AC: 1953 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1649 AN: 5166

South Asian (SAS) AF: 0.0414 AC: 200 AN: 4826

European-Finnish (FIN) AF: 0.0928 AC: 985 AN: 10610

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0339 AC: 2306 AN: 68014

Other (OTH) AF: 0.0491 AC: 104 AN: 2116

Alfa AF: 0.0396 Hom.: 35

Bravo AF: 0.0565

Asia WGS AF: 0.182 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.60
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs10483468; hg19: chr14-36923303;