rs13381188

chr18-53617480-C-T

Variant summary

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

The ENST00000654465.1(LINC01919):n.532+8121C>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 0.412 in 151,974 control chromosomes in the GnomAD database, including 13,527 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 0.41 (13527 hom., cov: 32)
• Consequence: LINC01919 ENST00000654465.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904304	XR_007066375.1	n.67-112160G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01919	ENST00000654465.1	n.532+8121C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62518 AN: 151856 Hom.: 13519 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.412 AC: 62546 AN: 151974 Hom.: 13527 Cov.: 32 AF XY: 0.416 AC XY: 30892 AN XY: 74258

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.452

Alfa AF: 0.408 Hom.: 2058

Bravo AF: 0.393

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.3
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13381188; hg19: chr18-51143850;