12-91990882-G-A

Variant names:

• chr12-91990882-G-A
• rs4608114
• ENST00000546975.4:n.223-1689C>T

Variant summary

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

The ENST00000546975.4(LINC01619):​n.223-1689C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,906 control chromosomes in the GnomAD database, including 14,878 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 0.43 (14878 hom., cov: 31)
• Consequence: LINC01619 ENST00000546975.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 6 publications found

Genes affected

LINC01619 (HGNC:27409): (long intergenic non-protein coding RNA 1619)

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 (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546975.4. 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
	LINC01619	NR_046159.2		n.224-520C>T		intron	N/A
	LINC01619	NR_046160.2		n.386-520C>T		intron	N/A
	LINC01619	NR_132339.1		n.386-1689C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01619	ENST00000546975.4	TSL:1	n.223-1689C>T		intron	N/A
	LINC01619	ENST00000551563.6	TSL:1	n.223-1689C>T		intron	N/A
	LINC01619	ENST00000551843.5	TSL:1	n.224-520C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65258 AN: 151788 Hom.: 14866 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.430 AC: 65306 AN: 151906 Hom.: 14878 Cov.: 31 AF XY: 0.427 AC XY: 31709 AN XY: 74236

African (AFR) AF: 0.531 AC: 21989 AN: 41426

American (AMR) AF: 0.405 AC: 6168 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1531 AN: 3464

East Asian (EAS) AF: 0.813 AC: 4191 AN: 5158

South Asian (SAS) AF: 0.333 AC: 1611 AN: 4832

European-Finnish (FIN) AF: 0.334 AC: 3526 AN: 10552

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24922 AN: 67908

Other (OTH) AF: 0.434 AC: 916 AN: 2112

Alfa AF: 0.387 Hom.: 20263

Bravo AF: 0.447

Asia WGS AF: 0.559 AC: 1941 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	0.48
DANN	Benign	0.28
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs4608114; hg19: chr12-92384658;