ENST00000654465.1:n.532+8121C>T

Variant names:

• chr18-53617480-C-T
• rs13381188
• ENST00000654465.1:n.532+8121C>T

Variant summary

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

The ENST00000654465.1(LINC01919):​n.532+8121C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.535 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.532+8121C>T		intron	N/A
	LINC01919	ENST00000655896.1		n.1061-12281C>T		intron	N/A
	LINC01919	ENST00000658566.1		n.480+8121C>T		intron	N/A

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

African (AFR) AF: 0.281 AC: 11664 AN: 41454

American (AMR) AF: 0.408 AC: 6232 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2017 AN: 5170

South Asian (SAS) AF: 0.553 AC: 2662 AN: 4816

European-Finnish (FIN) AF: 0.489 AC: 5151 AN: 10530

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31496 AN: 67956

Other (OTH) AF: 0.452 AC: 953 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs13381188; hg19: chr18-51143850;