rs12960296

Positions:

• chr18-53628530-G-T

Variant summary

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

The ENST00000654465.1(LINC01919):​n.533-1231G>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 0.443 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

Genes affected

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

LOC124904304 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124904304	XR_007066375.1	n.66+114855C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01919	ENST00000654465.1	n.533-1231G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.469

Alfa AF: 0.457 Hom.: 2046

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12960296; hg19: chr18-51154900;