rs10878630

Positions:

• chr12-67564920-G-A

Variant summary

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

The NR_103861.1(LINC02408):​n.154-594G>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 0.303 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 NR_103861.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02408	NR_103861.1	n.154-594G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02408	ENST00000650195.1	n.486+15756G>A		intron_variant, non_coding_transcript_variant
LINC02408	ENST00000400306.2	n.154-594G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.315

Alfa AF: 0.355 Hom.: 20380

Bravo AF: 0.292

Asia WGS AF: 0.277 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
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: rs10878630; hg19: chr12-67958700;