18-51023575-A-G

Variant names:

• chr18-51023575-A-G
• rs7244227
• ENST00000590722.2:n.158-23345A>G

Variant summary

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

The ENST00000590722.2(ENSG00000267699):​n.158-23345A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,088 control chromosomes in the GnomAD database, including 9,638 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 0.35 (9638 hom., cov: 32)
• Consequence: ENSG00000267699 ENST00000590722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267699	ENST00000590722.2	TSL:2	n.158-23345A>G		intron	N/A	ENSP00000465737.1
	ENSG00000267699	ENST00000588256.1	TSL:4	n.335-23345A>G		intron	N/A
	ENSG00000289868	ENST00000701227.2		n.255-3950T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53427 AN: 151970 Hom.: 9642 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.351 AC: 53456 AN: 152088 Hom.: 9638 Cov.: 32 AF XY: 0.351 AC XY: 26062 AN XY: 74328

African (AFR) AF: 0.285 AC: 11801 AN: 41472

American (AMR) AF: 0.356 AC: 5445 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1385 AN: 3466

East Asian (EAS) AF: 0.411 AC: 2123 AN: 5170

South Asian (SAS) AF: 0.246 AC: 1184 AN: 4822

European-Finnish (FIN) AF: 0.401 AC: 4236 AN: 10576

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25835 AN: 67984

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.372 Hom.: 41219

Bravo AF: 0.352

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.95
DANN	Benign	0.54
PhyloP100		-0.15
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: rs7244227; hg19: chr18-48549945;