1-55340792-T-C

Variant names:

• chr1-55340792-T-C
• rs207150
• ENST00000643167.1:n.138+11367T>C

Variant summary

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

The ENST00000643167.1(LINC01755):​n.138+11367T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 152,294 control chromosomes in the GnomAD database, including 67,693 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 0.94 (67693 hom., cov: 33)
• Consequence: LINC01755 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643167.1. 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	ENST00000643167.1		n.138+11367T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143348 AN: 152176 Hom.: 67636 Cov.: 33

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.942 AC: 143464 AN: 152294 Hom.: 67693 Cov.: 33 AF XY: 0.943 AC XY: 70211 AN XY: 74464

African (AFR) AF: 0.986 AC: 40999 AN: 41566

American (AMR) AF: 0.955 AC: 14613 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3104 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5181 AN: 5188

South Asian (SAS) AF: 0.968 AC: 4671 AN: 4824

European-Finnish (FIN) AF: 0.912 AC: 9664 AN: 10598

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62167 AN: 68026

Other (OTH) AF: 0.940 AC: 1987 AN: 2114

Alfa AF: 0.933 Hom.: 46940

Bravo AF: 0.947

Asia WGS AF: 0.983 AC: 3418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.82
PhyloP100		-0.54

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs207150;

hg19: chr1-55806465;