chr6-19785357-C-T

Variant names:

• chr6-19785357-C-T
• rs7739264
• ENST00000432171.2:n.263+53461G>A

Variant summary

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

The ENST00000432171.2(LNC-LBCS):​n.263+53461G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,846 control chromosomes in the GnomAD database, including 30,718 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 0.62 (30718 hom., cov: 31)
• Consequence: LNC-LBCS ENST00000432171.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 37 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNC-LBCS	NR_134651.1	n.155+16730G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNC-LBCS	ENST00000432171.2	n.263+53461G>A		intron_variant	Intron 1 of 4	3
LNC-LBCS	ENST00000445568.2	n.549+16730G>A		intron_variant	Intron 2 of 4	3
LNC-LBCS	ENST00000638138.1	n.183+16730G>A		intron_variant	Intron 2 of 6	5

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93674 AN: 151726 Hom.: 30667 Cov.: 31

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.618 AC: 93780 AN: 151846 Hom.: 30718 Cov.: 31 AF XY: 0.613 AC XY: 45503 AN XY: 74214

African (AFR) AF: 0.844 AC: 34997 AN: 41464

American (AMR) AF: 0.468 AC: 7139 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1794 AN: 3464

East Asian (EAS) AF: 0.736 AC: 3793 AN: 5154

South Asian (SAS) AF: 0.545 AC: 2621 AN: 4810

European-Finnish (FIN) AF: 0.542 AC: 5698 AN: 10516

Middle Eastern (MID) AF: 0.580 AC: 167 AN: 288

European-Non Finnish (NFE) AF: 0.529 AC: 35881 AN: 67892

Other (OTH) AF: 0.589 AC: 1240 AN: 2106

Alfa AF: 0.552 Hom.: 100287

Bravo AF: 0.622

Asia WGS AF: 0.636 AC: 2209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.089
DANN	Benign	0.45
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7739264; hg19: chr6-19785588;