1-55342470-C-T

Variant names:

• chr1-55342470-C-T
• rs207145
• ENST00000643167.1:n.138+13045C>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+13045C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,252 control chromosomes in the GnomAD database, including 61,917 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 0.90 (61917 hom., cov: 32)
• Consequence: LINC01755 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 6 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 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+13045C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137078 AN: 152134 Hom.: 61873 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.901 AC: 137183 AN: 152252 Hom.: 61917 Cov.: 32 AF XY: 0.902 AC XY: 67139 AN XY: 74432

African (AFR) AF: 0.949 AC: 39429 AN: 41564

American (AMR) AF: 0.907 AC: 13877 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2892 AN: 3468

East Asian (EAS) AF: 0.889 AC: 4603 AN: 5178

South Asian (SAS) AF: 0.924 AC: 4451 AN: 4816

European-Finnish (FIN) AF: 0.884 AC: 9369 AN: 10600

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59637 AN: 68010

Other (OTH) AF: 0.892 AC: 1883 AN: 2110

Alfa AF: 0.889 Hom.: 41919

Bravo AF: 0.903

Asia WGS AF: 0.898 AC: 3122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.17
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs207145; hg19: chr1-55808143;