rs10946320

Positions:

• chr6-19461323-T-C

Variant summary

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

The ENST00000653002.1(LNC-LBCS):​n.1036+73564A>G 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 0.312 in 152,080 control chromosomes in the GnomAD database, including 7,546 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 0.31 (7546 hom., cov: 32)
• Consequence: LNC-LBCS ENST00000653002.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LNC-LBCS	ENST00000653002.1	n.1036+73564A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47437 AN: 151962 Hom.: 7549 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.312 AC: 47450 AN: 152080 Hom.: 7546 Cov.: 32 AF XY: 0.313 AC XY: 23233 AN XY: 74318

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.308

Alfa AF: 0.316 Hom.: 1323

Bravo AF: 0.300

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.4
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: rs10946320; hg19: chr6-19461554;