1-55369757-C-T

Variant names:

• chr1-55369757-C-T
• rs12565257
• ENST00000643167.1:n.138+40332C>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+40332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,024 control chromosomes in the GnomAD database, including 28,793 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 0.61 (28793 hom., cov: 31)
• Consequence: LINC01755 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.641 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+40332C>T		intron	N/A
	LINC01755	ENST00000646341.1		n.158+8192C>T		intron	N/A
	LINC01755	ENST00000773165.1		n.153+8192C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93353 AN: 151906 Hom.: 28773 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.614 AC: 93414 AN: 152024 Hom.: 28793 Cov.: 31 AF XY: 0.613 AC XY: 45516 AN XY: 74310

African (AFR) AF: 0.607 AC: 25156 AN: 41456

American (AMR) AF: 0.564 AC: 8620 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1930 AN: 3472

East Asian (EAS) AF: 0.515 AC: 2656 AN: 5162

South Asian (SAS) AF: 0.660 AC: 3182 AN: 4818

European-Finnish (FIN) AF: 0.639 AC: 6751 AN: 10572

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43131 AN: 67950

Other (OTH) AF: 0.591 AC: 1246 AN: 2108

Alfa AF: 0.588 Hom.: 7603

Bravo AF: 0.605

Asia WGS AF: 0.620 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.84
PhyloP100		-0.57

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: rs12565257;

hg19: chr1-55835430;

COSMIC: COSV70432393;