rs13381188

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904304	XR_007066375.1	n.67-112160G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01919	ENST00000654465.1	n.532+8121C>T		intron_variant	Intron 5 of 5
LINC01919	ENST00000655896.1	n.1061-12281C>T		intron_variant	Intron 4 of 4
LINC01919	ENST00000658566.1	n.480+8121C>T		intron_variant	Intron 5 of 5

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 v4.3

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;