ENST00000581556.2:n.745+23024C>T

Variant names:

• chr18-1206983-C-T
• rs1826508
• ENST00000581556.2:n.745+23024C>T

Variant summary

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

The ENST00000581556.2(ENSG00000263551):​n.745+23024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,028 control chromosomes in the GnomAD database, including 51,320 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 0.79 (51320 hom., cov: 32)
• Consequence: ENSG00000263551 ENST00000581556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 4 publications found

Genes affected

ENSG00000263551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581556.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000263551	ENST00000581556.2	TSL:4	n.745+23024C>T		intron	N/A
	ENSG00000263551	ENST00000670380.1		n.732+23024C>T		intron	N/A
	ENSG00000263551	ENST00000753289.1		n.703+23024C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120179 AN: 151910 Hom.: 51310 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.791 AC: 120225 AN: 152028 Hom.: 51320 Cov.: 32 AF XY: 0.795 AC XY: 59088 AN XY: 74330

African (AFR) AF: 0.435 AC: 17991 AN: 41334

American (AMR) AF: 0.893 AC: 13643 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3129 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4211 AN: 5168

South Asian (SAS) AF: 0.882 AC: 4256 AN: 4828

European-Finnish (FIN) AF: 0.961 AC: 10194 AN: 10610

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63935 AN: 68020

Other (OTH) AF: 0.825 AC: 1743 AN: 2112

Alfa AF: 0.839 Hom.: 18435

Bravo AF: 0.770

Asia WGS AF: 0.826 AC: 2872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1826508; hg19: chr18-1206984;