chr6-19821550-A-G

Variant names:

• chr6-19821550-A-G
• rs12527834
• ENST00000432171.2:n.263+17268T>C

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+17268T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0684 in 152,332 control chromosomes in the GnomAD database, including 411 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 0.068 (411 hom., cov: 33)
• Consequence: LNC-LBCS ENST00000432171.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0901 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNC-LBCS	ENST00000432171.2	TSL:3	n.263+17268T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10408 AN: 152214 Hom.: 411 Cov.: 33

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.0684 AC: 10415 AN: 152332 Hom.: 411 Cov.: 33 AF XY: 0.0680 AC XY: 5064 AN XY: 74490

African (AFR) AF: 0.0287 AC: 1193 AN: 41588

American (AMR) AF: 0.0774 AC: 1185 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5182

South Asian (SAS) AF: 0.0433 AC: 209 AN: 4830

European-Finnish (FIN) AF: 0.0912 AC: 968 AN: 10618

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0920 AC: 6256 AN: 68020

Other (OTH) AF: 0.0875 AC: 185 AN: 2114

Alfa AF: 0.0881 Hom.: 1101

Bravo AF: 0.0660

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.45
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12527834; hg19: chr6-19821781;