1-55642931-A-G

Variant names:

• chr1-55642931-A-G
• rs1165472
• ENST00000422374.1:n.240+27929A>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+27929A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,122 control chromosomes in the GnomAD database, including 5,418 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 0.26 (5418 hom., cov: 31)
• Consequence: LINC01755 ENST00000422374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 13 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01755	ENST00000422374.1	TSL:2	n.240+27929A>G		intron	N/A
	LINC01755	ENST00000634769.2	TSL:5	n.216+27929A>G		intron	N/A
	LINC01755	ENST00000643167.1		n.220+27929A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39499 AN: 152004 Hom.: 5418 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.260 AC: 39514 AN: 152122 Hom.: 5418 Cov.: 31 AF XY: 0.256 AC XY: 19024 AN XY: 74364

African (AFR) AF: 0.298 AC: 12350 AN: 41492

American (AMR) AF: 0.183 AC: 2799 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 762 AN: 3472

East Asian (EAS) AF: 0.114 AC: 588 AN: 5180

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4816

European-Finnish (FIN) AF: 0.229 AC: 2419 AN: 10584

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18141 AN: 67982

Other (OTH) AF: 0.252 AC: 532 AN: 2112

Alfa AF: 0.266 Hom.: 8668

Bravo AF: 0.257

Asia WGS AF: 0.261 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.96
DANN	Benign	0.72
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1165472; hg19: chr1-56108604;