rs11151630

chr18-56190750-C-A

Variant summary

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

The NR_148972.1(LINC03069):n.499+14G>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 0.325 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: LINC03069 NR_148972.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC03069	NR_148972.1	n.499+14G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03069	ENST00000382897.2	n.499+14G>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 NFE exome AF: 0.00

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

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.318

Alfa AF: 0.288 Hom.: 10183

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11151630; hg19: chr18-53857981;