ENST00000625325.2:n.294-3426G>A

Variant names:

• chr10-25713319-G-A
• rs2504183
• ENST00000625325.2:n.294-3426G>A

Variant summary

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

The ENST00000625325.2(LINC00836):​n.294-3426G>A variant causes a intron 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 ENST00000625325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 3 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=-0.85).
• 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 rank	MANE	Protein	UniProt
LINC00836	NR_108067.1	n.350-3426G>A		intron_variant	Intron 3 of 4
LINC00836	NR_108068.1	n.89-3426G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00836	ENST00000625325.2	n.294-3426G>A		intron_variant	Intron 3 of 4	4
LINC00836	ENST00000626230.2	n.89-3426G>A		intron_variant	Intron 1 of 2	2
LINC00836	ENST00000648557.1	n.583-3426G>A		intron_variant	Intron 6 of 7

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

African (AFR) AF: 0.137 AC: 5673 AN: 41374

American (AMR) AF: 0.178 AC: 2715 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3464

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5174

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4810

European-Finnish (FIN) AF: 0.203 AC: 2111 AN: 10382

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17411 AN: 67886

Other (OTH) AF: 0.222 AC: 468 AN: 2104

Alfa AF: 0.211 Hom.: 2566

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2504183; hg19: chr10-26002248;