6-19399266-G-A

Variant names:

• chr6-19399266-G-A
• rs6918297
• ENST00000636202.1:n.852-1729C>T

Variant summary

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

The ENST00000636202.1(LNC-LBCS):​n.852-1729C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,786 control chromosomes in the GnomAD database, including 14,289 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 0.43 (14289 hom., cov: 32)
• Consequence: LNC-LBCS ENST00000636202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636202.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNC-LBCS	ENST00000636202.1	TSL:5	n.852-1729C>T		intron	N/A
	LNC-LBCS	ENST00000653002.1		n.1037-73468C>T		intron	N/A
	LNC-LBCS	ENST00000660410.1		n.883-36442C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64728 AN: 151668 Hom.: 14262 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.427 AC: 64800 AN: 151786 Hom.: 14289 Cov.: 32 AF XY: 0.437 AC XY: 32389 AN XY: 74172

African (AFR) AF: 0.482 AC: 19919 AN: 41328

American (AMR) AF: 0.509 AC: 7780 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1239 AN: 3472

East Asian (EAS) AF: 0.513 AC: 2633 AN: 5134

South Asian (SAS) AF: 0.584 AC: 2807 AN: 4808

European-Finnish (FIN) AF: 0.434 AC: 4567 AN: 10518

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24651 AN: 67944

Other (OTH) AF: 0.405 AC: 852 AN: 2104

Alfa AF: 0.396 Hom.: 4767

Bravo AF: 0.433

Asia WGS AF: 0.564 AC: 1966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.62
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6918297; hg19: chr6-19399497;