18-5311893-C-T

Variant names:

• chr18-5311893-C-T
• rs589398
• ENST00000579113.1:n.57+1441C>T

Variant summary

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

The ENST00000579113.1(ENSG00000264254):​n.57+1441C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.982 in 152,298 control chromosomes in the GnomAD database, including 73,409 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 0.98 (73409 hom., cov: 32)
• Consequence: ENSG00000264254 ENST00000579113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 2 publications found

Genes affected

ENSG00000264254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579113.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000264254	ENST00000579113.1	TSL:4	n.57+1441C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.982 AC: 149409 AN: 152180 Hom.: 73351 Cov.: 32

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.982 AC: 149526 AN: 152298 Hom.: 73409 Cov.: 32 AF XY: 0.983 AC XY: 73200 AN XY: 74462

African (AFR) AF: 0.993 AC: 41267 AN: 41554

American (AMR) AF: 0.980 AC: 14985 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 3379 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5165 AN: 5166

South Asian (SAS) AF: 0.994 AC: 4797 AN: 4828

European-Finnish (FIN) AF: 0.992 AC: 10540 AN: 10622

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66190 AN: 68040

Other (OTH) AF: 0.967 AC: 2044 AN: 2114

Alfa AF: 0.980 Hom.: 8649

Bravo AF: 0.981

Asia WGS AF: 0.994 AC: 3456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.34
PhyloP100		-0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs589398;

hg19: chr18-5311892;