chr18-55757127-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-27772C>T		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000587346.1	n.140-4176C>T		intron_variant	Intron 1 of 4	4
ENSG00000267284	ENST00000589662.1	n.218-27772C>T		intron_variant	Intron 1 of 3	5
ENSG00000267284	ENST00000592936.1	n.473-1913C>T		intron_variant	Intron 1 of 1	4
ENSG00000267284	ENST00000654829.1	n.157-27772C>T		intron_variant	Intron 2 of 8

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

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.796

Alfa AF: 0.760 Hom.: 8547

Bravo AF: 0.763

Asia WGS AF: 0.678 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4800996; hg19: chr18-53424358;