18-11494200-T-C

Variant names:

• chr18-11494200-T-C
• rs1455244
• ENST00000586947.7:n.250+3959T>C

Variant summary

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

The ENST00000586947.7(LINC01255):​n.250+3959T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,134 control chromosomes in the GnomAD database, including 22,432 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 0.51 (22432 hom., cov: 33)
• Consequence: LINC01255 ENST00000586947.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 9 publications found

Genes affected

LINC01255 (HGNC:49871): (long intergenic non-protein coding RNA 1255)

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 (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586947.7. 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
	LINC01255	NR_110778.1		n.194+3959T>C		intron	N/A
	LINC01255	NR_110779.1		n.115+5278T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01255	ENST00000586947.7	TSL:2	n.250+3959T>C		intron	N/A
	LINC01255	ENST00000587189.6	TSL:4	n.115+5278T>C		intron	N/A
	LINC01255	ENST00000589566.1	TSL:4	n.168+3959T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.513 AC: 78015 AN: 152016 Hom.: 22371 Cov.: 33

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.514 AC: 78139 AN: 152134 Hom.: 22432 Cov.: 33 AF XY: 0.520 AC XY: 38652 AN XY: 74370

African (AFR) AF: 0.751 AC: 31148 AN: 41502

American (AMR) AF: 0.561 AC: 8574 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3466

East Asian (EAS) AF: 0.703 AC: 3638 AN: 5178

South Asian (SAS) AF: 0.516 AC: 2486 AN: 4820

European-Finnish (FIN) AF: 0.453 AC: 4796 AN: 10578

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24216 AN: 67986

Other (OTH) AF: 0.509 AC: 1074 AN: 2112

Alfa AF: 0.497 Hom.: 13889

Bravo AF: 0.532

Asia WGS AF: 0.640 AC: 2223 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.56
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1455244; hg19: chr18-11494199;