rs2015252

Variant names:

• chr1-55407107-C-T
• rs2015252
• ENST00000643167.1:n.138+77682C>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+77682C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,146 control chromosomes in the GnomAD database, including 13,679 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 0.41 (13679 hom., cov: 33)
• Consequence: LINC01755 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01755	ENST00000643167.1	n.138+77682C>T		intron_variant	Intron 1 of 3
LINC01755	ENST00000646341.1	n.158+45542C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62967 AN: 152028 Hom.: 13667 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.414 AC: 62995 AN: 152146 Hom.: 13679 Cov.: 33 AF XY: 0.413 AC XY: 30738 AN XY: 74384

African (AFR) AF: 0.298 AC: 12375 AN: 41510

American (AMR) AF: 0.508 AC: 7771 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1823 AN: 3472

East Asian (EAS) AF: 0.430 AC: 2221 AN: 5168

South Asian (SAS) AF: 0.325 AC: 1568 AN: 4832

European-Finnish (FIN) AF: 0.426 AC: 4501 AN: 10568

Middle Eastern (MID) AF: 0.445 AC: 129 AN: 290

European-Non Finnish (NFE) AF: 0.462 AC: 31430 AN: 67996

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.445 Hom.: 41949

Bravo AF: 0.414

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.39
DANN	Benign	0.24
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2015252; hg19: chr1-55872780;