rs2553377

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01091	ENST00000662928.1	n.546-40455C>A		intron_variant	Intron 1 of 3
LINC01091	ENST00000664622.1	n.212-40459C>A		intron_variant	Intron 1 of 8
LINC01091	ENST00000666328.1	n.637-40455C>A		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.0320

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.126

Alfa AF: 0.156 Hom.: 951

Bravo AF: 0.120

Asia WGS AF: 0.162 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2553377; hg19: chr4-124533487;