rs12065953

Variant names:

• chr1-55427766-C-T
• rs12065953
• ENST00000643167.1:n.138+98341C>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+98341C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,138 control chromosomes in the GnomAD database, including 1,794 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 0.11 (1794 hom., cov: 32)
• Consequence: LINC01755 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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+98341C>T		intron	N/A
	LINC01755	ENST00000646341.1		n.158+66201C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16502 AN: 152020 Hom.: 1788 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.0434

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.109 AC: 16539 AN: 152138 Hom.: 1794 Cov.: 32 AF XY: 0.106 AC XY: 7863 AN XY: 74382

African (AFR) AF: 0.287 AC: 11878 AN: 41432

American (AMR) AF: 0.0518 AC: 793 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0649 AC: 225 AN: 3468

East Asian (EAS) AF: 0.0927 AC: 479 AN: 5166

South Asian (SAS) AF: 0.0437 AC: 211 AN: 4830

European-Finnish (FIN) AF: 0.0252 AC: 267 AN: 10602

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2470 AN: 68018

Other (OTH) AF: 0.0857 AC: 181 AN: 2112

Alfa AF: 0.0482 Hom.: 350

Bravo AF: 0.117

Asia WGS AF: 0.0940 AC: 326 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	0.046
DANN	Benign	0.57
PhyloP100		-1.5

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: rs12065953;

hg19: chr1-55893439;