12-126983603-T-C

Variant names:

• chr12-126983603-T-C
• rs1147262
• ENST00000512624.6:n.607-7686A>G

Variant summary

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

The ENST00000512624.6(LINC02405):​n.607-7686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 152,240 control chromosomes in the GnomAD database, including 1,487 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 0.084 (1487 hom., cov: 32)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 1 publications found

Genes affected

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

LOC105370063 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512624.6. 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
	LINC02405	NR_104646.1		n.607-7686A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02405	ENST00000512624.6	TSL:1	n.607-7686A>G		intron	N/A
	LINC02405	ENST00000651439.2		n.653-7686A>G		intron	N/A
	LINC02405	ENST00000656033.1		n.621-7686A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0832 AC: 12653 AN: 152120 Hom.: 1469 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00567

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0835 AC: 12715 AN: 152240 Hom.: 1487 Cov.: 32 AF XY: 0.0824 AC XY: 6139 AN XY: 74460

African (AFR) AF: 0.260 AC: 10780 AN: 41498

American (AMR) AF: 0.0346 AC: 530 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.107 AC: 555 AN: 5174

South Asian (SAS) AF: 0.0286 AC: 138 AN: 4828

European-Finnish (FIN) AF: 0.00235 AC: 25 AN: 10630

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

European-Non Finnish (NFE) AF: 0.00567 AC: 386 AN: 68022

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0449 Hom.: 154

Bravo AF: 0.0964

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.47
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1147262; hg19: chr12-127468148;