ENST00000601836.1:c.-444+12745C>G

Variant names:

• chr5-55009883-G-C
• rs2194205
• ENST00000601836.1:c.-444+12745C>G

Variant summary

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

The ENST00000601836.1(ESM1):​c.-444+12745C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,010 control chromosomes in the GnomAD database, including 37,557 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 0.69 (37557 hom., cov: 32)
• Consequence: ESM1 ENST00000601836.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

Genes affected

ESM1 (HGNC:3466): (endothelial cell specific molecule 1) This gene encodes a secreted protein which is mainly expressed in the endothelial cells in human lung and kidney tissues. The expression of this gene is regulated by cytokines, suggesting that it may play a role in endothelium-dependent pathological disorders. The transcript contains multiple polyadenylation and mRNA instability signals. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 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
ESM1	ENST00000601836.1	c.-444+12745C>G		intron_variant	Intron 1 of 1	5		ENSP00000471642.1
ESM1	ENST00000598310.5	n.44+12745C>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104522 AN: 151892 Hom.: 37502 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.688 AC: 104638 AN: 152010 Hom.: 37557 Cov.: 32 AF XY: 0.689 AC XY: 51165 AN XY: 74288

African (AFR) AF: 0.897 AC: 37238 AN: 41522

American (AMR) AF: 0.728 AC: 11117 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2097 AN: 3468

East Asian (EAS) AF: 0.663 AC: 3425 AN: 5166

South Asian (SAS) AF: 0.637 AC: 3072 AN: 4824

European-Finnish (FIN) AF: 0.593 AC: 6246 AN: 10536

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.578 AC: 39280 AN: 67906

Other (OTH) AF: 0.668 AC: 1409 AN: 2108

Alfa AF: 0.635 Hom.: 3988

Bravo AF: 0.710

Asia WGS AF: 0.684 AC: 2379 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.25
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2194205; hg19: chr5-54305711;