18-51026855-C-G

Variant names:

• chr18-51026855-C-G
• rs4939650
• ENST00000590722.2:n.158-20065C>G

Variant summary

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

The ENST00000590722.2(ENSG00000267699):​n.158-20065C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,018 control chromosomes in the GnomAD database, including 13,793 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 0.42 (13793 hom., cov: 32)
• Consequence: ENSG00000267699 ENST00000590722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 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.158-20065C>G		intron	N/A	ENSP00000465737.1
	ENSG00000267699	ENST00000588256.1	TSL:4	n.335-20065C>G		intron	N/A
	ENSG00000289868	ENST00000701227.2		n.254+3063G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64326 AN: 151900 Hom.: 13776 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.424 AC: 64406 AN: 152018 Hom.: 13793 Cov.: 32 AF XY: 0.421 AC XY: 31271 AN XY: 74308

African (AFR) AF: 0.495 AC: 20513 AN: 41460

American (AMR) AF: 0.403 AC: 6159 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1454 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2348 AN: 5172

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4818

European-Finnish (FIN) AF: 0.406 AC: 4289 AN: 10558

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26783 AN: 67962

Other (OTH) AF: 0.442 AC: 930 AN: 2106

Alfa AF: 0.394 Hom.: 1484

Bravo AF: 0.435

Asia WGS AF: 0.384 AC: 1333 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	0.81
DANN	Benign	0.36
PhyloP100		-0.085
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: rs4939650; hg19: chr18-48553225;