rs7773456

Variant names:

• chr6-19823007-T-G
• rs7773456
• ENST00000432171.2:n.263+15811A>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+15811A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,964 control chromosomes in the GnomAD database, including 9,835 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 0.35 (9835 hom., cov: 32)
• Consequence: LNC-LBCS ENST00000432171.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNC-LBCS	ENST00000432171.2	n.263+15811A>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53031 AN: 151844 Hom.: 9820 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.349 AC: 53080 AN: 151964 Hom.: 9835 Cov.: 32 AF XY: 0.344 AC XY: 25589 AN XY: 74294

African (AFR) AF: 0.473 AC: 19599 AN: 41418

American (AMR) AF: 0.238 AC: 3638 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2136 AN: 5124

South Asian (SAS) AF: 0.315 AC: 1515 AN: 4814

European-Finnish (FIN) AF: 0.282 AC: 2989 AN: 10584

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21244 AN: 67952

Other (OTH) AF: 0.314 AC: 661 AN: 2108

Alfa AF: 0.320 Hom.: 6927

Bravo AF: 0.351

Asia WGS AF: 0.368 AC: 1280 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	2.8
DANN	Benign	0.39
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7773456; hg19: chr6-19823238;