ENST00000745030.1:n.646-1114C>T

Variant names:

• chr18-56263975-C-T
• rs1237238
• ENST00000745030.1:n.646-1114C>T

Variant summary

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

The ENST00000745030.1(ENSG00000297056):​n.646-1114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 151,994 control chromosomes in the GnomAD database, including 40,771 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 0.73 (40771 hom., cov: 30)
• Consequence: ENSG00000297056 ENST00000745030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 4 publications found

Genes affected

ENSG00000297056 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 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
ENSG00000297056	ENST00000745030.1	n.646-1114C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110489 AN: 151876 Hom.: 40721 Cov.: 30

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.728 AC: 110600 AN: 151994 Hom.: 40771 Cov.: 30 AF XY: 0.726 AC XY: 53934 AN XY: 74254

African (AFR) AF: 0.822 AC: 34095 AN: 41480

American (AMR) AF: 0.743 AC: 11350 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2410 AN: 3472

East Asian (EAS) AF: 0.928 AC: 4784 AN: 5154

South Asian (SAS) AF: 0.601 AC: 2890 AN: 4806

European-Finnish (FIN) AF: 0.655 AC: 6909 AN: 10546

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.674 AC: 45775 AN: 67952

Other (OTH) AF: 0.724 AC: 1529 AN: 2112

Alfa AF: 0.698 Hom.: 142246

Bravo AF: 0.742

Asia WGS AF: 0.780 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.35
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1237238; hg19: chr18-53931206;