rs2553377

Variant names:

• chr4-123612332-C-A
• rs2553377
• ENST00000662928.1:n.546-40455C>A

Variant summary

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

The ENST00000662928.1(LINC01091):​n.546-40455C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,100 control chromosomes in the GnomAD database, including 1,749 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 0.13 (1749 hom., cov: 32)
• Consequence: LINC01091 ENST00000662928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 2 publications found

Genes affected

LINC01091 (HGNC:27721): (long intergenic non-protein coding RNA 1091)

ENSG00000304190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662928.1. 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
	LINC01091	ENST00000662928.1		n.546-40455C>A		intron	N/A
	LINC01091	ENST00000664622.1		n.212-40459C>A		intron	N/A
	LINC01091	ENST00000666328.1		n.637-40455C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20395 AN: 151982 Hom.: 1752 Cov.: 32

Gnomad AFR AF: 0.0318

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.134 AC: 20396 AN: 152100 Hom.: 1749 Cov.: 32 AF XY: 0.140 AC XY: 10385 AN XY: 74338

African (AFR) AF: 0.0320 AC: 1328 AN: 41522

American (AMR) AF: 0.157 AC: 2404 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3468

East Asian (EAS) AF: 0.167 AC: 861 AN: 5158

South Asian (SAS) AF: 0.203 AC: 977 AN: 4814

European-Finnish (FIN) AF: 0.240 AC: 2536 AN: 10562

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11451 AN: 67984

Other (OTH) AF: 0.126 AC: 266 AN: 2110

Alfa AF: 0.155 Hom.: 1050

Bravo AF: 0.120

Asia WGS AF: 0.162 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.23
PhyloP100		-0.49

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: rs2553377;

hg19: chr4-124533487;