10-25670053-G-T

Position:

• chr10-25670053-G-T

Variant summary

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

The NR_108067.1(LINC00836):​n.262+17011G>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 0.411 in 151,900 control chromosomes in the GnomAD database, including 13,913 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 0.41 (13913 hom., cov: 32)
• Consequence: LINC00836 NR_108067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00836	NR_108067.1	n.262+17011G>T		intron_variant, non_coding_transcript_variant
LINC00836	NR_108068.1	n.88+18254G>T		intron_variant, non_coding_transcript_variant
LINC00836	NR_108069.1	n.377+1723G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00836	ENST00000626230.2	n.88+18254G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62378 AN: 151782 Hom.: 13896 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.411 AC: 62438 AN: 151900 Hom.: 13913 Cov.: 32 AF XY: 0.409 AC XY: 30387 AN XY: 74208

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.369

Alfa AF: 0.347 Hom.: 19261

Bravo AF: 0.413

Asia WGS AF: 0.203 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6482510; hg19: chr10-25958982;