ENST00000512624.6:n.685+3427G>A

Variant names:

• chr12-126972412-C-T
• rs1344361
• ENST00000512624.6:n.685+3427G>A

Variant summary

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

The ENST00000512624.6(LINC02405):​n.685+3427G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,194 control chromosomes in the GnomAD database, including 2,059 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 0.097 (2059 hom., cov: 32)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 0 publications found

Genes affected

LINC02405 (HGNC:53333): (long intergenic non-protein coding RNA 2405)

ENSG00000298504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02405	NR_104646.1	n.685+3427G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02405	ENST00000512624.6	n.685+3427G>A		intron_variant	Intron 4 of 6	1
ENSG00000298504	ENST00000756029.1	n.165C>T		non_coding_transcript_exon_variant	Exon 1 of 3
LINC02405	ENST00000651439.2	n.731+3427G>A		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14715 AN: 152074 Hom.: 2041 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0380

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00603

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0971 AC: 14778 AN: 152194 Hom.: 2059 Cov.: 32 AF XY: 0.0958 AC XY: 7129 AN XY: 74430

African (AFR) AF: 0.305 AC: 12658 AN: 41482

American (AMR) AF: 0.0411 AC: 628 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0380 AC: 132 AN: 3470

East Asian (EAS) AF: 0.106 AC: 550 AN: 5170

South Asian (SAS) AF: 0.0365 AC: 176 AN: 4822

European-Finnish (FIN) AF: 0.00254 AC: 27 AN: 10610

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00603 AC: 410 AN: 68028

Other (OTH) AF: 0.0833 AC: 176 AN: 2112

Alfa AF: 0.0201 Hom.: 41

Bravo AF: 0.112

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.89
DANN	Benign	0.25
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1344361; hg19: chr12-127456957;