rs10483468

Positions:

• chr14-36454098-T-C

Variant summary

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

The ENST00000634305.1(ENSG00000283098):​n.322+5261T>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 0.0537 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: ENST00000634305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634305.1	n.322+5261T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0221

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.0928

Gnomad4 NFE AF: 0.0339

Gnomad4 OTH AF: 0.0491

Alfa AF: 0.0401 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483468; hg19: chr14-36923303;