18-56050233-C-T

Variant names:

• chr18-56050233-C-T
• rs2286812
• ENST00000382897.2:n.1067+5672G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000382897.2(LINC01539):​n.1067+5672G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,136 control chromosomes in the GnomAD database, including 943 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 0.10 (943 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01539 ENST00000382897.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 13 publications found

Genes affected

LINC01539 (HGNC:51307): (long intergenic non-protein coding RNA 1539)

LINC01905 (HGNC:52724): (long intergenic non-protein coding RNA 1905)

LINC03069 (HGNC:56641): (long intergenic non-protein coding RNA 3069)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01905	NR_146510.1	n.165+56C>T		intron_variant	Intron 2 of 3
LINC01905	NR_146511.1	n.165+56C>T		intron_variant	Intron 2 of 2
LINC03069	NR_148972.1	n.1067+5672G>A		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01539	ENST00000382897.2	n.1067+5672G>A		intron_variant	Intron 6 of 8	2
LINC01905	ENST00000585684.6	n.285+7889C>T		intron_variant	Intron 1 of 1	2
LINC01905	ENST00000589450.5	n.49+56C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15709 AN: 152016 Hom.: 941 Cov.: 32

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0968

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.119

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.103 AC: 15706 AN: 152136 Hom.: 943 Cov.: 32 AF XY: 0.103 AC XY: 7690 AN XY: 74360

African (AFR) AF: 0.0512 AC: 2127 AN: 41542

American (AMR) AF: 0.114 AC: 1745 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0968 AC: 336 AN: 3470

East Asian (EAS) AF: 0.128 AC: 664 AN: 5174

South Asian (SAS) AF: 0.183 AC: 878 AN: 4810

European-Finnish (FIN) AF: 0.0847 AC: 896 AN: 10576

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8538 AN: 67970

Other (OTH) AF: 0.118 AC: 250 AN: 2110

Alfa AF: 0.123 Hom.: 2298

Bravo AF: 0.103

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	19
DANN	Benign	0.71
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2286812; hg19: chr18-53717464;