rs17483277

chr6-19790340-G-Achr6-19790340-G-T

Variant summary

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

The NR_134651.1(LNC-LBCS):n.155+11747C>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 0.323 in 151,994 control chromosomes in the GnomAD database, including 7,958 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 0.32 (7958 hom., cov: 32)
• Consequence: LNC-LBCS NR_134651.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

LNC-LBCS (HGNC:54418): (lncRNA bladder and prostate cancer suppressor, hnRNPK interacting)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LNC-LBCS	NR_134651.1	n.155+11747C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LNC-LBCS	ENST00000653002.1	n.471-4900C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49011 AN: 151876 Hom.: 7954 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.313

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.323 AC: 49053 AN: 151994 Hom.: 7958 Cov.: 32 AF XY: 0.322 AC XY: 23942 AN XY: 74314

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.313

Alfa AF: 0.299 Hom.: 5432

Bravo AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.1
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17483277; hg19: chr6-19790571;