6-19790340-G-A

Variant names:

• chr6-19790340-G-A
• rs17483277
• ENST00000432171.2:n.263+48478C>T

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+48478C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,994 control chromosomes in the GnomAD database, including 7,958 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 0.32 (7958 hom., cov: 32)
• Consequence: LNC-LBCS ENST00000432171.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNC-LBCS	NR_134651.1		n.155+11747C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNC-LBCS	ENST00000432171.2	TSL:3	n.263+48478C>T		intron	N/A
	LNC-LBCS	ENST00000445568.2	TSL:3	n.549+11747C>T		intron	N/A
	LNC-LBCS	ENST00000638138.1	TSL:5	n.183+11747C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49011 AN: 151876 Hom.: 7954 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.323 AC: 49053 AN: 151994 Hom.: 7958 Cov.: 32 AF XY: 0.322 AC XY: 23942 AN XY: 74314

African (AFR) AF: 0.336 AC: 13941 AN: 41440

American (AMR) AF: 0.295 AC: 4509 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2170 AN: 5160

South Asian (SAS) AF: 0.312 AC: 1501 AN: 4814

European-Finnish (FIN) AF: 0.340 AC: 3588 AN: 10568

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21312 AN: 67966

Other (OTH) AF: 0.313 AC: 660 AN: 2110

Alfa AF: 0.306 Hom.: 8544

Bravo AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs17483277; hg19: chr6-19790571;