rs12960296

Variant names:

• chr18-53628530-G-T
• rs12960296
• ENST00000654465.1:n.533-1231G>T

Variant summary

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

The ENST00000654465.1(LINC01919):​n.533-1231G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,818 control chromosomes in the GnomAD database, including 15,552 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 0.44 (15552 hom., cov: 31)
• Consequence: LINC01919 ENST00000654465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 1 publications found

Genes affected

LINC01919 (HGNC:52739): (long intergenic non-protein coding RNA 1919)

LOC124904304 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654465.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01919	ENST00000654465.1		n.533-1231G>T		intron	N/A
	LINC01919	ENST00000655896.1		n.1061-1231G>T		intron	N/A
	LINC01919	ENST00000658566.1		n.481-1231G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67263 AN: 151700 Hom.: 15551 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.443 AC: 67288 AN: 151818 Hom.: 15552 Cov.: 31 AF XY: 0.447 AC XY: 33138 AN XY: 74148

African (AFR) AF: 0.315 AC: 13050 AN: 41396

American (AMR) AF: 0.424 AC: 6462 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1907 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2029 AN: 5140

South Asian (SAS) AF: 0.567 AC: 2730 AN: 4812

European-Finnish (FIN) AF: 0.539 AC: 5664 AN: 10506

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33835 AN: 67926

Other (OTH) AF: 0.469 AC: 989 AN: 2108

Alfa AF: 0.450 Hom.: 2079

Bravo AF: 0.423

Asia WGS AF: 0.467 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.52
PhyloP100		0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12960296;

hg19: chr18-51154900;