18-5311893-C-T

Position:

• chr18-5311893-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000579113.1(ENSG00000264254):​n.57+1441C>T variant causes a intron, non coding transcript 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: ENST00000579113.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985144	XR_001753330.2	n.225+128C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000579113.1	n.57+1441C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.993

Gnomad4 AMR AF: 0.980

Gnomad4 ASJ AF: 0.973

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.967

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs589398; hg19: chr18-5311892;