ENST00000634769.2:n.275-58676T>A

Variant names:

• chr1-55773588-T-A
• rs753978
• ENST00000634769.2:n.275-58676T>A

Variant summary

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

The ENST00000634769.2(LINC01755):​n.275-58676T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,024 control chromosomes in the GnomAD database, including 18,582 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 0.49 (18582 hom., cov: 33)
• Consequence: LINC01755 ENST00000634769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634769.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01755	ENST00000634769.2	TSL:5	n.275-58676T>A		intron	N/A
	LINC01755	ENST00000643167.1		n.279-58676T>A		intron	N/A
	LINC01755	ENST00000646341.1		n.299-58676T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74310 AN: 151906 Hom.: 18570 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.489 AC: 74357 AN: 152024 Hom.: 18582 Cov.: 33 AF XY: 0.491 AC XY: 36500 AN XY: 74302

African (AFR) AF: 0.579 AC: 24005 AN: 41440

American (AMR) AF: 0.373 AC: 5704 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3472

East Asian (EAS) AF: 0.688 AC: 3563 AN: 5178

South Asian (SAS) AF: 0.595 AC: 2866 AN: 4818

European-Finnish (FIN) AF: 0.483 AC: 5091 AN: 10550

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29857 AN: 67974

Other (OTH) AF: 0.478 AC: 1009 AN: 2112

Alfa AF: 0.315 Hom.: 760

Bravo AF: 0.483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs753978; hg19: chr1-56239261;