rs10946320

Variant names:

• chr6-19461323-T-C
• rs10946320
• ENST00000636202.1:n.852-63786A>G

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+73564A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779
• Publications: 2 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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 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.852-63786A>G		intron	N/A
	LNC-LBCS	ENST00000653002.1		n.1036+73564A>G		intron	N/A
	LNC-LBCS	ENST00000660410.1		n.882+73564A>G		intron	N/A

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

African (AFR) AF: 0.272 AC: 11285 AN: 41488

American (AMR) AF: 0.275 AC: 4203 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5178

South Asian (SAS) AF: 0.303 AC: 1457 AN: 4816

European-Finnish (FIN) AF: 0.423 AC: 4458 AN: 10550

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22894 AN: 67978

Other (OTH) AF: 0.308 AC: 650 AN: 2112

Alfa AF: 0.314 Hom.: 1349

Bravo AF: 0.300

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.4
DANN	Benign	0.83
PhyloP100		-0.78

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10946320;

hg19: chr6-19461554;