6-19759356-T-C

Variant names:

• chr6-19759356-T-C
• rs9295448
• ENST00000432171.2:n.263+79462A>G

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+79462A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,048 control chromosomes in the GnomAD database, including 5,056 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 0.25 (5056 hom., cov: 32)
• Consequence: LNC-LBCS ENST00000432171.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 6 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=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432171.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNC-LBCS	NR_134651.1		n.156-9598A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNC-LBCS	ENST00000432171.2	TSL:3	n.263+79462A>G		intron	N/A
	LNC-LBCS	ENST00000445568.2	TSL:3	n.550-9598A>G		intron	N/A
	LNC-LBCS	ENST00000638138.1	TSL:5	n.184-9598A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37524 AN: 151930 Hom.: 5049 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.247 AC: 37541 AN: 152048 Hom.: 5056 Cov.: 32 AF XY: 0.247 AC XY: 18350 AN XY: 74328

African (AFR) AF: 0.179 AC: 7432 AN: 41472

American (AMR) AF: 0.214 AC: 3271 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3470

East Asian (EAS) AF: 0.579 AC: 2988 AN: 5158

South Asian (SAS) AF: 0.297 AC: 1432 AN: 4816

European-Finnish (FIN) AF: 0.270 AC: 2852 AN: 10572

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18268 AN: 67972

Other (OTH) AF: 0.223 AC: 472 AN: 2112

Alfa AF: 0.259 Hom.: 22695

Bravo AF: 0.239

Asia WGS AF: 0.374 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9295448;

hg19: chr6-19759587;