ENST00000555300.1:n.19-7493C>T

Variant names:

• chr14-24615475-C-T
• rs11158813
• ENST00000555300.1:n.19-7493C>T

Variant summary

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

The ENST00000555300.1(ENSG00000258657):​n.19-7493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0836 in 152,056 control chromosomes in the GnomAD database, including 555 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 0.084 (555 hom., cov: 32)
• Consequence: ENSG00000258657 ENST00000555300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 4 publications found

Genes affected

ENSG00000258657 (HGNC:58166):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 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
ENSG00000258657	ENST00000555300.1	n.19-7493C>T		intron_variant	Intron 1 of 3	5
ENSG00000258657	ENST00000557736.5	n.281-7493C>T		intron_variant	Intron 1 of 2	4
ENSG00000258657	ENST00000770595.1	n.76-7493C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0836 AC: 12701 AN: 151938 Hom.: 550 Cov.: 32

Gnomad AFR AF: 0.0673

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0663

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0745

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0970

Gnomad OTH AF: 0.0940

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

GnomAD4 genome AF: 0.0836 AC: 12714 AN: 152056 Hom.: 555 Cov.: 32 AF XY: 0.0825 AC XY: 6135 AN XY: 74334

African (AFR) AF: 0.0674 AC: 2793 AN: 41458

American (AMR) AF: 0.0661 AC: 1010 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3466

East Asian (EAS) AF: 0.0617 AC: 319 AN: 5174

South Asian (SAS) AF: 0.132 AC: 633 AN: 4812

European-Finnish (FIN) AF: 0.0745 AC: 787 AN: 10558

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0970 AC: 6598 AN: 68002

Other (OTH) AF: 0.0925 AC: 195 AN: 2108

Alfa AF: 0.0939 Hom.: 934

Bravo AF: 0.0815

Asia WGS AF: 0.0750 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.90
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11158813; hg19: chr14-25084681;