18-55757127-C-T

Variant names:

• chr18-55757127-C-T
• rs4800996
• ENST00000587346.1:n.140-4176C>T

Variant summary

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

The ENST00000587346.1(ENSG00000267284):​n.140-4176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,062 control chromosomes in the GnomAD database, including 43,807 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 0.76 (43807 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 3 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587346.1. 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
	ENSG00000267284	ENST00000587346.1	TSL:4	n.140-4176C>T		intron	N/A
	ENSG00000267284	ENST00000589662.1	TSL:5	n.218-27772C>T		intron	N/A
	ENSG00000267284	ENST00000592936.1	TSL:4	n.473-1913C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.757 AC: 114985 AN: 151944 Hom.: 43783 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.757 AC: 115055 AN: 152062 Hom.: 43807 Cov.: 32 AF XY: 0.759 AC XY: 56367 AN XY: 74312

African (AFR) AF: 0.679 AC: 28151 AN: 41446

American (AMR) AF: 0.866 AC: 13238 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3470

East Asian (EAS) AF: 0.639 AC: 3296 AN: 5156

South Asian (SAS) AF: 0.612 AC: 2951 AN: 4822

European-Finnish (FIN) AF: 0.816 AC: 8626 AN: 10574

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53410 AN: 67994

Other (OTH) AF: 0.796 AC: 1680 AN: 2110

Alfa AF: 0.757 Hom.: 8719

Bravo AF: 0.763

Asia WGS AF: 0.678 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.64
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs4800996; hg19: chr18-53424358;