10-25683081-T-C

Position:

• chr10-25683081-T-C

Variant summary

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

The NR_108067.1(LINC00836):​n.263-12786T>C 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 0.497 in 151,978 control chromosomes in the GnomAD database, including 21,287 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 0.50 (21287 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00836 NR_108067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743

Genes affected

LINC00836 (HGNC:44915): (long intergenic non-protein coding RNA 836)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00836	NR_108067.1	n.263-12786T>C		intron_variant, non_coding_transcript_variant
LINC00836	NR_108069.1	n.938T>C		non_coding_transcript_exon_variant	4/4
LINC00836	NR_108068.1	n.88+31282T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00836	ENST00000626230.2	n.88+31282T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75484 AN: 151860 Hom.: 21239 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.456

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.497 AC: 75596 AN: 151978 Hom.: 21287 Cov.: 32 AF XY: 0.494 AC XY: 36712 AN XY: 74286

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.457

Alfa AF: 0.392 Hom.: 15633

Bravo AF: 0.509

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2290167; hg19: chr10-25972010;