rs10498696

Positions:

• chr6-19452396-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_134615.1(LOC105374960):​n.96+2480C>T 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 0.0261 in 152,236 control chromosomes in the GnomAD database, including 51 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 0.026 (51 hom., cov: 32)
• Consequence: LOC105374960 NR_134615.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

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

LOC105374960 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0261 (3969/152236) while in subpopulation AFR AF= 0.0318 (1323/41540). AF 95% confidence interval is 0.0304. There are 51 homozygotes in gnomad4. There are 1872 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 51 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374960	NR_134615.1	n.96+2480C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNC-LBCS	ENST00000653002.1	n.1036+82491G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0261 AC: 3968 AN: 152118 Hom.: 51 Cov.: 32

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0294

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0114

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0261 AC: 3969 AN: 152236 Hom.: 51 Cov.: 32 AF XY: 0.0252 AC XY: 1872 AN XY: 74430

Gnomad4 AFR AF: 0.0318

Gnomad4 AMR AF: 0.0294

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0114

Gnomad4 NFE AF: 0.0265

Gnomad4 OTH AF: 0.0266

Alfa AF: 0.0251 Hom.: 7

Bravo AF: 0.0271

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.018
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498696; hg19: chr6-19452627;