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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904304	XR_007066375.1	n.66+114855C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01919	ENST00000654465.1	n.533-1231G>T		intron_variant	Intron 5 of 5
LINC01919	ENST00000655896.1	n.1061-1231G>T		intron_variant	Intron 4 of 4
LINC01919	ENST00000658566.1	n.481-1231G>T		intron_variant	Intron 5 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs12960296; hg19: chr18-51154900;