1-55446511-C-T

Variant names:

• chr1-55446511-C-T
• rs1986518
• ENST00000643167.1:n.138+117086C>T

Variant summary

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

The ENST00000643167.1(LINC01755):​n.138+117086C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,026 control chromosomes in the GnomAD database, including 19,494 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 0.50 (19494 hom., cov: 32)
• Consequence: LINC01755 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 publications found

Genes affected

LINC01755 (HGNC:52543): (long intergenic non-protein coding RNA 1755)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643167.1. 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
	LINC01755	ENST00000643167.1		n.138+117086C>T		intron	N/A
	LINC01755	ENST00000646341.1		n.158+84946C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76294 AN: 151908 Hom.: 19468 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.502 AC: 76357 AN: 152026 Hom.: 19494 Cov.: 32 AF XY: 0.502 AC XY: 37270 AN XY: 74300

African (AFR) AF: 0.477 AC: 19765 AN: 41444

American (AMR) AF: 0.515 AC: 7865 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2117 AN: 5160

South Asian (SAS) AF: 0.351 AC: 1694 AN: 4822

European-Finnish (FIN) AF: 0.579 AC: 6112 AN: 10556

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35795 AN: 67976

Other (OTH) AF: 0.476 AC: 1007 AN: 2114

Alfa AF: 0.513 Hom.: 10305

Bravo AF: 0.498

Asia WGS AF: 0.344 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.86
DANN	Benign	0.79
PhyloP100		-1.1

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: rs1986518;

hg19: chr1-55912184;