chr1-55835227-G-A

Variant names:

• chr1-55835227-G-A
• rs11587235
• ENST00000424357.1:n.257+2802G>A

Variant summary

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

The ENST00000424357.1(LINC01755):​n.257+2802G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0723 in 152,150 control chromosomes in the GnomAD database, including 468 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 0.072 (468 hom., cov: 33)
• Consequence: LINC01755 ENST00000424357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 2 publications found

Genes affected

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

ENSG00000297153 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424357.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01755	ENST00000424357.1	TSL:3	n.257+2802G>A		intron	N/A
	LINC01755	ENST00000646266.1		n.248+2802G>A		intron	N/A
	LINC01755	ENST00000659410.1		n.267+2802G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10977 AN: 152032 Hom.: 464 Cov.: 33

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0723 AC: 11001 AN: 152150 Hom.: 468 Cov.: 33 AF XY: 0.0730 AC XY: 5429 AN XY: 74394

African (AFR) AF: 0.0899 AC: 3732 AN: 41530

American (AMR) AF: 0.0419 AC: 640 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3468

East Asian (EAS) AF: 0.143 AC: 741 AN: 5176

South Asian (SAS) AF: 0.0298 AC: 144 AN: 4830

European-Finnish (FIN) AF: 0.0993 AC: 1050 AN: 10574

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0651 AC: 4426 AN: 67982

Other (OTH) AF: 0.0620 AC: 131 AN: 2114

Alfa AF: 0.0727 Hom.: 61

Bravo AF: 0.0686

Asia WGS AF: 0.0790 AC: 276 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.59
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11587235; hg19: chr1-56300900;