4-123926085-C-T

Variant names:

• chr4-123926085-C-T
• rs1878989
• ENST00000508111.6:n.738+748C>T

Variant summary

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

The ENST00000511919.6(LINC01091):​n.809+748C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,022 control chromosomes in the GnomAD database, including 4,030 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 0.21 (4030 hom., cov: 32)
• Consequence: LINC01091 ENST00000511919.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511919.6. 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
	LINC01091	NR_027105.3		n.783+748C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01091	ENST00000508111.6	TSL:5	n.738+748C>T		intron	N/A
	LINC01091	ENST00000511919.6	TSL:3	n.809+748C>T		intron	N/A
	LINC01091	ENST00000655571.1		n.478+748C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31356 AN: 151902 Hom.: 4029 Cov.: 32

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.206 AC: 31348 AN: 152022 Hom.: 4030 Cov.: 32 AF XY: 0.217 AC XY: 16101 AN XY: 74296

African (AFR) AF: 0.0566 AC: 2349 AN: 41528

American (AMR) AF: 0.304 AC: 4635 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1763 AN: 5146

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4814

European-Finnish (FIN) AF: 0.306 AC: 3228 AN: 10564

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.235 AC: 15984 AN: 67940

Other (OTH) AF: 0.209 AC: 441 AN: 2108

Alfa AF: 0.224 Hom.: 6865

Bravo AF: 0.194

Asia WGS AF: 0.309 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.68
DANN	Benign	0.68
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1878989; hg19: chr4-124847240;