rs16882214

Variant names:

• chr6-19443704-C-G
• rs16882214
• ENST00000636202.1:n.852-46167G>C

Variant summary

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

The ENST00000653002.1(LNC-LBCS):​n.1036+91183G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,170 control chromosomes in the GnomAD database, including 1,555 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 0.12 (1555 hom., cov: 33)
• Consequence: LNC-LBCS ENST00000653002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 15 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653002.1. 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	ENST00000636202.1	TSL:5	n.852-46167G>C		intron	N/A
	LNC-LBCS	ENST00000653002.1		n.1036+91183G>C		intron	N/A
	LNC-LBCS	ENST00000660410.1		n.883-80880G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18768 AN: 152052 Hom.: 1551 Cov.: 33

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.123 AC: 18782 AN: 152170 Hom.: 1555 Cov.: 33 AF XY: 0.132 AC XY: 9823 AN XY: 74388

African (AFR) AF: 0.0262 AC: 1088 AN: 41528

American (AMR) AF: 0.201 AC: 3071 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3472

East Asian (EAS) AF: 0.133 AC: 688 AN: 5182

South Asian (SAS) AF: 0.267 AC: 1289 AN: 4824

European-Finnish (FIN) AF: 0.214 AC: 2258 AN: 10574

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9431 AN: 67992

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.136 Hom.: 206

Bravo AF: 0.115

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.17
DANN	Benign	0.78
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs16882214; hg19: chr6-19443935;