rs6907340

Positions:

• chr6-19803537-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134651.1(LNC-LBCS):​n.85+1138G>A variant causes a intron, non coding transcript 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 NR_134651.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

Genes affected

LNC-LBCS (HGNC:54418): (lncRNA bladder and prostate cancer suppressor, hnRNPK interacting)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LNC-LBCS	NR_134651.1	n.85+1138G>A		intron_variant, non_coding_transcript_variant
LNC-LBCS	NR_134649.1	n.567G>A		non_coding_transcript_exon_variant	3/3
LNC-LBCS	NR_134650.1	n.459G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNC-LBCS	ENST00000653002.1	n.400+634G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.638

Gnomad4 AMR exome AF: 0.329

Gnomad4 ASJ exome AF: 0.372

Gnomad4 EAS exome AF: 0.670

Gnomad4 SAS exome AF: 0.432

Gnomad4 FIN exome AF: 0.439

Gnomad4 NFE exome AF: 0.372

Gnomad4 OTH exome AF: 0.421

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

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.453

Alfa AF: 0.387 Hom.: 23571

Bravo AF: 0.465

Asia WGS AF: 0.538 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6907340; hg19: chr6-19803768;