6-19452433-T-C

Variant names:

• chr6-19452433-T-C
• rs9295438
• ENST00000636202.1:n.852-54896A>G

Variant summary

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

The ENST00000636202.1(LNC-LBCS):​n.852-54896A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,114 control chromosomes in the GnomAD database, including 46,764 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 0.77 (46764 hom., cov: 32)
• Consequence: LNC-LBCS ENST00000636202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 4 publications found

Genes affected

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

ENSG00000301784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374960	NR_134615.1	n.96+2517T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNC-LBCS	ENST00000636202.1	n.852-54896A>G		intron_variant	Intron 7 of 9	5
LNC-LBCS	ENST00000653002.1	n.1036+82454A>G		intron_variant	Intron 8 of 8
LNC-LBCS	ENST00000660410.1	n.882+82454A>G		intron_variant	Intron 8 of 8

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116442 AN: 151996 Hom.: 46757 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.925

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.766 AC: 116486 AN: 152114 Hom.: 46764 Cov.: 32 AF XY: 0.766 AC XY: 56990 AN XY: 74374

African (AFR) AF: 0.513 AC: 21241 AN: 41442

American (AMR) AF: 0.748 AC: 11440 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3051 AN: 3464

East Asian (EAS) AF: 0.720 AC: 3722 AN: 5166

South Asian (SAS) AF: 0.698 AC: 3362 AN: 4820

European-Finnish (FIN) AF: 0.925 AC: 9808 AN: 10604

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61096 AN: 68004

Other (OTH) AF: 0.776 AC: 1641 AN: 2116

Alfa AF: 0.858 Hom.: 88387

Bravo AF: 0.743

Asia WGS AF: 0.680 AC: 2362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.66
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs9295438; hg19: chr6-19452664;