rs2580128

Variant names:

• chr18-1804896-C-T
• rs2580128
• ENST00000653094.1:n.326-19882C>T

Variant summary

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

The ENST00000653094.1(ENSG00000266602):​n.326-19882C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,032 control chromosomes in the GnomAD database, including 3,595 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 0.19 (3595 hom., cov: 32)
• Consequence: ENSG00000266602 ENST00000653094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 1 publications found

Genes affected

ENSG00000266602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 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
ENSG00000266602	ENST00000653094.1	n.326-19882C>T		intron_variant	Intron 3 of 5
ENSG00000266602	ENST00000653330.1	n.252-19882C>T		intron_variant	Intron 2 of 4
ENSG00000266602	ENST00000655815.1	n.252-19882C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29071 AN: 151914 Hom.: 3592 Cov.: 32

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.191 AC: 29068 AN: 152032 Hom.: 3595 Cov.: 32 AF XY: 0.190 AC XY: 14114 AN XY: 74296

African (AFR) AF: 0.0498 AC: 2069 AN: 41526

American (AMR) AF: 0.185 AC: 2827 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3466

East Asian (EAS) AF: 0.155 AC: 800 AN: 5162

South Asian (SAS) AF: 0.227 AC: 1094 AN: 4818

European-Finnish (FIN) AF: 0.265 AC: 2797 AN: 10566

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17871 AN: 67932

Other (OTH) AF: 0.202 AC: 427 AN: 2110

Alfa AF: 0.232 Hom.: 5879

Bravo AF: 0.177

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.25
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2580128; hg19: chr18-1804897;