rs10878630

Variant names:

• chr12-67564920-G-A
• rs10878630
• ENST00000400306.2:n.154-594G>A

Variant summary

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

The ENST00000400306.2(LINC02408):​n.154-594G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,870 control chromosomes in the GnomAD database, including 7,425 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 0.30 (7425 hom., cov: 32)
• Consequence: LINC02408 ENST00000400306.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 5 publications found

Genes affected

LINC02408 (HGNC:53337): (long intergenic non-protein coding RNA 2408)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400306.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02408	NR_103861.1		n.154-594G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02408	ENST00000400306.2	TSL:2	n.154-594G>A		intron	N/A
	LINC02408	ENST00000650195.1		n.486+15756G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45948 AN: 151752 Hom.: 7420 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.303 AC: 45951 AN: 151870 Hom.: 7425 Cov.: 32 AF XY: 0.302 AC XY: 22379 AN XY: 74208

African (AFR) AF: 0.198 AC: 8219 AN: 41410

American (AMR) AF: 0.289 AC: 4405 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1194 AN: 5174

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4814

European-Finnish (FIN) AF: 0.342 AC: 3594 AN: 10508

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.359 AC: 24403 AN: 67942

Other (OTH) AF: 0.315 AC: 662 AN: 2104

Alfa AF: 0.346 Hom.: 42190

Bravo AF: 0.292

Asia WGS AF: 0.277 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.68
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs10878630; hg19: chr12-67958700;