rs11151630

Variant names:

• chr18-56190750-C-A
• rs11151630
• ENST00000382897.2:n.499+14G>T

Variant summary

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

The ENST00000382897.2(LINC01539):​n.499+14G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,000 control chromosomes in the GnomAD database, including 8,369 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 0.33 (8369 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: -0.0980
• Publications: 5 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03069	NR_148972.1	n.499+14G>T		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01539	ENST00000382897.2	n.499+14G>T		intron_variant	Intron 1 of 8	2
LINC01539	ENST00000765110.1	n.157+14G>T		intron_variant	Intron 1 of 3
LINC01539	ENST00000765111.1	n.155+14G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49367 AN: 151884 Hom.: 8350 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.320

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.325 AC: 49425 AN: 152000 Hom.: 8369 Cov.: 32 AF XY: 0.323 AC XY: 24012 AN XY: 74306

African (AFR) AF: 0.403 AC: 16703 AN: 41432

American (AMR) AF: 0.338 AC: 5168 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3472

East Asian (EAS) AF: 0.156 AC: 809 AN: 5176

South Asian (SAS) AF: 0.340 AC: 1639 AN: 4814

European-Finnish (FIN) AF: 0.286 AC: 3017 AN: 10558

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19764 AN: 67952

Other (OTH) AF: 0.318 AC: 669 AN: 2106

Alfa AF: 0.299 Hom.: 25053

Bravo AF: 0.334

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.34
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs11151630; hg19: chr18-53857981;