rs2504183

chr10-25713319-G-Achr10-25713319-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.350-3426G>A 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 0.203 in 151,632 control chromosomes in the GnomAD database, including 3,440 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 0.20 (3440 hom., cov: 32)
• Consequence: LINC00836 NR_108067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00836	NR_108067.1	n.350-3426G>A		intron_variant, non_coding_transcript_variant
LINC00836	NR_108068.1	n.89-3426G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00836	ENST00000626230.2	n.89-3426G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30714 AN: 151518 Hom.: 3438 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.203 AC: 30741 AN: 151632 Hom.: 3440 Cov.: 32 AF XY: 0.200 AC XY: 14850 AN XY: 74126

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.222

Alfa AF: 0.208 Hom.: 1602

Bravo AF: 0.194

Asia WGS AF: 0.154 AC: 536 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.4
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2504183; hg19: chr10-26002248;