ENST00000554665.1:n.257-20153C>T

Variant names:

• chr14-30755252-G-A
• rs179562
• ENST00000554665.1:n.257-20153C>T

Variant summary

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

The ENST00000554665.1(ENSG00000258558):​n.257-20153C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,008 control chromosomes in the GnomAD database, including 32,545 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 0.62 (32545 hom., cov: 31)
• Consequence: ENSG00000258558 ENST00000554665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

Genes affected

ENSG00000258558 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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
ENSG00000258558	ENST00000554665.1	n.257-20153C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93884 AN: 151890 Hom.: 32549 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.618 AC: 93891 AN: 152008 Hom.: 32545 Cov.: 31 AF XY: 0.619 AC XY: 46013 AN XY: 74312

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.648

Alfa AF: 0.741 Hom.: 40968

Bravo AF: 0.587

Asia WGS AF: 0.635 AC: 2210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs179562; hg19: chr14-31224458;