rs4134425

Variant names:

• chr14-40076250-T-C
• rs4134425
• ENST00000650911.1:n.418-51320T>C

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.418-51320T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,832 control chromosomes in the GnomAD database, including 35,624 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 0.68 (35624 hom., cov: 32)
• Consequence: ENSG00000258526 ENST00000650911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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
ENSG00000258526	ENST00000650911.1	n.418-51320T>C		intron_variant	Intron 3 of 5
ENSG00000258526	ENST00000651829.1	n.1619-262T>C		intron_variant	Intron 13 of 13
ENSG00000258526	ENST00000652126.1	n.458-51320T>C		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103484 AN: 151714 Hom.: 35588 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.682 AC: 103570 AN: 151832 Hom.: 35624 Cov.: 32 AF XY: 0.679 AC XY: 50361 AN XY: 74154

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.685

Alfa AF: 0.685 Hom.: 7297

Bravo AF: 0.677

Asia WGS AF: 0.536 AC: 1864 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4134425; hg19: chr14-40545454; COSMIC: COSV51317436;