10-25670053-G-T

Variant names:

• chr10-25670053-G-T
• rs6482510
• ENST00000625325.2:n.206+17011G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000625325.2(LINC00836):​n.206+17011G>T variant causes a intron 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 ENST00000625325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000625325.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00836	NR_108067.1		n.262+17011G>T		intron	N/A
	LINC00836	NR_108068.1		n.88+18254G>T		intron	N/A
	LINC00836	NR_108069.1		n.377+1723G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00836	ENST00000625325.2	TSL:4	n.206+17011G>T		intron	N/A
	LINC00836	ENST00000626230.2	TSL:2	n.88+18254G>T		intron	N/A
	LINC00836	ENST00000628620.1	TSL:5	n.314+1723G>T		intron	N/A

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

African (AFR) AF: 0.577 AC: 23885 AN: 41400

American (AMR) AF: 0.383 AC: 5851 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3472

East Asian (EAS) AF: 0.121 AC: 626 AN: 5162

South Asian (SAS) AF: 0.228 AC: 1093 AN: 4798

European-Finnish (FIN) AF: 0.474 AC: 5002 AN: 10544

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23926 AN: 67934

Other (OTH) AF: 0.369 AC: 779 AN: 2112

Alfa AF: 0.359 Hom.: 43540

Bravo AF: 0.413

Asia WGS AF: 0.203 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs6482510; hg19: chr10-25958982;