rs4608114

chr12-91990882-G-Achr12-91990882-G-Cchr12-91990882-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_132340.1(LINC01619):n.386-1689C>T variant causes a intron, non coding transcript 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 NR_132340.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01619	NR_132340.1	n.386-1689C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01619	ENST00000549802.5	n.226-1689C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.434

Alfa AF: 0.382 Hom.: 15527

Bravo AF: 0.447

Asia WGS AF: 0.559 AC: 1941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.48
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4608114; hg19: chr12-92384658;