18-51022369-A-T

Variant names:

• chr18-51022369-A-T
• rs1787111
• ENST00000590722.2:n.158-24551A>T

Variant summary

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

The ENST00000590722.2(ENSG00000267699):​n.158-24551A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 152,304 control chromosomes in the GnomAD database, including 70,935 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 0.96 (70935 hom., cov: 31)
• Consequence: ENSG00000267699 ENST00000590722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 1 publications found

Genes affected

ENSG00000267699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590722.2. 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
	ENSG00000267699	ENST00000590722.2	TSL:2	n.158-24551A>T		intron	N/A	ENSP00000465737.1
	ENSG00000267699	ENST00000588256.1	TSL:4	n.335-24551A>T		intron	N/A
	ENSG00000289868	ENST00000701227.2		n.255-2744T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146810 AN: 152186 Hom.: 70877 Cov.: 31

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.965 AC: 146927 AN: 152304 Hom.: 70935 Cov.: 31 AF XY: 0.964 AC XY: 71804 AN XY: 74470

African (AFR) AF: 0.991 AC: 41220 AN: 41574

American (AMR) AF: 0.974 AC: 14910 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3358 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5173 AN: 5176

South Asian (SAS) AF: 0.937 AC: 4514 AN: 4820

European-Finnish (FIN) AF: 0.937 AC: 9943 AN: 10612

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64559 AN: 68026

Other (OTH) AF: 0.975 AC: 2061 AN: 2114

Alfa AF: 0.955 Hom.: 8623

Bravo AF: 0.971

Asia WGS AF: 0.975 AC: 3388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.40
PhyloP100		-0.42
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1787111; hg19: chr18-48548739;