rs1899384

Positions:

• chr18-53577519-T-C

Variant summary

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

The ENST00000579506.2(LINC01919):​n.213T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,100 control chromosomes in the GnomAD database, including 8,207 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 0.27 (8207 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC01919 ENST00000579506.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

Genes affected

LINC01919 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01919	NR_110798.1	n.105-554T>C		intron_variant
LOC124904304	XR_007066375.1	n.67-72199A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01919	ENST00000579506.2	n.213T>C		non_coding_transcript_exon_variant	2/2	3
LINC01919	ENST00000655896.1	n.181T>C		non_coding_transcript_exon_variant	2/5
LINC01919	ENST00000669727.1	n.205T>C		non_coding_transcript_exon_variant	2/4

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40354 AN: 151978 Hom.: 8183 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.216

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.266 AC: 40416 AN: 152098 Hom.: 8207 Cov.: 32 AF XY: 0.262 AC XY: 19503 AN XY: 74366

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.214

Alfa AF: 0.164 Hom.: 4014

Bravo AF: 0.279

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1899384; hg19: chr18-51103889;