1-55650559-C-G

Variant names:

• chr1-55650559-C-G
• rs1514135
• ENST00000422374.1:n.240+35557C>G

Variant summary

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

The ENST00000422374.1(LINC01755):​n.240+35557C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,012 control chromosomes in the GnomAD database, including 16,512 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 0.44 (16512 hom., cov: 32)
• Consequence: LINC01755 ENST00000422374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 4 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422374.1. 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	ENST00000422374.1	TSL:2	n.240+35557C>G		intron	N/A
	LINC01755	ENST00000634769.2	TSL:5	n.217-22701C>G		intron	N/A
	LINC01755	ENST00000643167.1		n.221-22701C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67476 AN: 151894 Hom.: 16480 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.444 AC: 67568 AN: 152012 Hom.: 16512 Cov.: 32 AF XY: 0.445 AC XY: 33079 AN XY: 74290

African (AFR) AF: 0.661 AC: 27393 AN: 41456

American (AMR) AF: 0.404 AC: 6172 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1634 AN: 5150

South Asian (SAS) AF: 0.412 AC: 1985 AN: 4814

European-Finnish (FIN) AF: 0.392 AC: 4136 AN: 10554

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24056 AN: 67972

Other (OTH) AF: 0.396 AC: 837 AN: 2114

Alfa AF: 0.398 Hom.: 1583

Bravo AF: 0.456

Asia WGS AF: 0.436 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.67
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1514135; hg19: chr1-56116232;