ENST00000557251.1:n.167-980T>C

Variant names:

• chr14-42702125-T-C
• rs1627411
• ENST00000557251.1:n.167-980T>C

Variant summary

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

The ENST00000557251.1(ENSG00000258394):​n.167-980T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,002 control chromosomes in the GnomAD database, including 43,693 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 0.75 (43693 hom., cov: 31)
• Consequence: ENSG00000258394 ENST00000557251.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

Genes affected

ENSG00000258394 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 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
ENSG00000258394	ENST00000557251.1	n.167-980T>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114201 AN: 151884 Hom.: 43655 Cov.: 31

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.752 AC: 114296 AN: 152002 Hom.: 43693 Cov.: 31 AF XY: 0.753 AC XY: 55913 AN XY: 74272

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.774

Alfa AF: 0.801 Hom.: 59822

Bravo AF: 0.743

Asia WGS AF: 0.684 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1627411; hg19: chr14-43171328;