ENST00000662928.1:n.546-7978C>T

Variant names:

• chr4-123644809-C-T
• rs1425419
• ENST00000662928.1:n.546-7978C>T

Variant summary

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

The ENST00000662928.1(LINC01091):​n.546-7978C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,136 control chromosomes in the GnomAD database, including 2,786 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 0.16 (2786 hom., cov: 31)
• Consequence: LINC01091 ENST00000662928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01091	ENST00000662928.1		n.546-7978C>T		intron	N/A
	LINC01091	ENST00000664622.1		n.212-7982C>T		intron	N/A
	LINC01091	ENST00000666328.1		n.637-7978C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24422 AN: 152018 Hom.: 2792 Cov.: 31

Gnomad AFR AF: 0.0419

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.160 AC: 24405 AN: 152136 Hom.: 2786 Cov.: 31 AF XY: 0.174 AC XY: 12906 AN XY: 74344

African (AFR) AF: 0.0417 AC: 1733 AN: 41552

American (AMR) AF: 0.296 AC: 4524 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1725 AN: 5160

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4818

European-Finnish (FIN) AF: 0.269 AC: 2842 AN: 10564

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10721 AN: 67982

Other (OTH) AF: 0.151 AC: 319 AN: 2110

Alfa AF: 0.158 Hom.: 4035

Bravo AF: 0.154

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.7
DANN	Benign	0.69
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1425419; hg19: chr4-124565964;