chr1-55973656-A-C

Variant names:

• chr1-55973656-A-C
• rs6664825
• ENST00000646266.1:n.465-1672A>C

Variant summary

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

The ENST00000646266.1(LINC01755):​n.465-1672A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 150,936 control chromosomes in the GnomAD database, including 5,257 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 0.27 (5257 hom., cov: 32)
• Consequence: LINC01755 ENST00000646266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 2 publications found

Genes affected

LINC01755 (HGNC:52543): (long intergenic non-protein coding RNA 1755)

LOC105378737 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646266.1. 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	ENST00000646266.1		n.465-1672A>C		intron	N/A
	LINC01755	ENST00000661225.1		n.293-1672A>C		intron	N/A
	LINC01755	ENST00000717013.1		n.320+11667A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 39999 AN: 150824 Hom.: 5247 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.265 AC: 40031 AN: 150936 Hom.: 5257 Cov.: 32 AF XY: 0.265 AC XY: 19535 AN XY: 73804

African (AFR) AF: 0.261 AC: 10543 AN: 40366

American (AMR) AF: 0.229 AC: 3493 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1815 AN: 5166

South Asian (SAS) AF: 0.313 AC: 1510 AN: 4826

European-Finnish (FIN) AF: 0.237 AC: 2504 AN: 10580

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18120 AN: 67946

Other (OTH) AF: 0.288 AC: 607 AN: 2106

Alfa AF: 0.212 Hom.: 881

Bravo AF: 0.264

Asia WGS AF: 0.305 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.54
PhyloP100		-0.74

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: rs6664825;

hg19: chr1-56439329;