ENST00000432171.2:n.263+17268T>C

Variant names:

• chr6-19821550-A-G
• rs12527834
• ENST00000432171.2:n.263+17268T>C

Variant summary

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

The ENST00000432171.2(LNC-LBCS):​n.263+17268T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0684 in 152,332 control chromosomes in the GnomAD database, including 411 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 0.068 (411 hom., cov: 33)
• Consequence: LNC-LBCS ENST00000432171.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNC-LBCS	ENST00000432171.2	n.263+17268T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10408 AN: 152214 Hom.: 411 Cov.: 33

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.0684 AC: 10415 AN: 152332 Hom.: 411 Cov.: 33 AF XY: 0.0680 AC XY: 5064 AN XY: 74490

Gnomad4 AFR AF: 0.0287

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0433

Gnomad4 FIN AF: 0.0912

Gnomad4 NFE AF: 0.0920

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0908 Hom.: 903

Bravo AF: 0.0660

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12527834; hg19: chr6-19821781;