chr6-19803537-C-T

Variant names:

• chr6-19803537-C-T
• rs6907340
• ENST00000447250.1:n.850G>A

Variant summary

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

The ENST00000447250.1(LNC-LBCS):​n.850G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 275,856 control chromosomes in the GnomAD database, including 28,852 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 0.46 (17545 hom., cov: 33)
  • Exomes 𝑓: 0.41 (11307 hom.)
• Consequence: LNC-LBCS ENST00000447250.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 14 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447250.1. 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
	LNC-LBCS	NR_134649.1		n.567G>A		non_coding_transcript_exon	Exon 3 of 3
	LNC-LBCS	NR_134650.1		n.459G>A		non_coding_transcript_exon	Exon 2 of 2
	LNC-LBCS	NR_134651.1		n.85+1138G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNC-LBCS	ENST00000447250.1	TSL:2	n.850G>A		non_coding_transcript_exon	Exon 2 of 2
	LNC-LBCS	ENST00000457670.3	TSL:2	n.637G>A		non_coding_transcript_exon	Exon 2 of 2
	LNC-LBCS	ENST00000607810.6	TSL:5	n.579G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70567 AN: 151894 Hom.: 17507 Cov.: 33

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.453

GnomAD4 exome AF: 0.415 AC: 51375 AN: 123844 Hom.: 11307 Cov.: 0 AF XY: 0.414 AC XY: 25843 AN XY: 62464

African (AFR) AF: 0.638 AC: 2724 AN: 4272

American (AMR) AF: 0.329 AC: 1245 AN: 3784

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1918 AN: 5160

East Asian (EAS) AF: 0.670 AC: 7301 AN: 10900

South Asian (SAS) AF: 0.432 AC: 493 AN: 1142

European-Finnish (FIN) AF: 0.439 AC: 3240 AN: 7388

Middle Eastern (MID) AF: 0.474 AC: 309 AN: 652

European-Non Finnish (NFE) AF: 0.372 AC: 30439 AN: 81734

Other (OTH) AF: 0.421 AC: 3706 AN: 8812

GnomAD4 genome AF: 0.465 AC: 70658 AN: 152012 Hom.: 17545 Cov.: 33 AF XY: 0.466 AC XY: 34617 AN XY: 74292

African (AFR) AF: 0.636 AC: 26365 AN: 41436

American (AMR) AF: 0.362 AC: 5522 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3468

East Asian (EAS) AF: 0.652 AC: 3366 AN: 5162

South Asian (SAS) AF: 0.425 AC: 2048 AN: 4816

European-Finnish (FIN) AF: 0.450 AC: 4753 AN: 10568

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25871 AN: 67978

Other (OTH) AF: 0.453 AC: 956 AN: 2110

Alfa AF: 0.402 Hom.: 56221

Bravo AF: 0.465

Asia WGS AF: 0.538 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.8
DANN	Benign	0.83
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6907340; hg19: chr6-19803768;