12-126943942-G-T

Variant names:

• chr12-126943942-G-T
• rs10773343
• ENST00000512624.6:n.686-20737C>A

Variant summary

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

The ENST00000512624.6(LINC02405):​n.686-20737C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,046 control chromosomes in the GnomAD database, including 13,551 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 0.40 (13551 hom., cov: 32)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996
• Publications: 0 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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.686-20737C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02405	ENST00000512624.6	TSL:1	n.686-20737C>A		intron	N/A
	LINC02405	ENST00000651439.2		n.732-20737C>A		intron	N/A
	LINC02405	ENST00000656033.1		n.700-20737C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61311 AN: 151928 Hom.: 13551 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.403 AC: 61313 AN: 152046 Hom.: 13551 Cov.: 32 AF XY: 0.401 AC XY: 29789 AN XY: 74326

African (AFR) AF: 0.222 AC: 9219 AN: 41486

American (AMR) AF: 0.350 AC: 5343 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1984 AN: 5168

South Asian (SAS) AF: 0.458 AC: 2204 AN: 4814

European-Finnish (FIN) AF: 0.530 AC: 5589 AN: 10554

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33849 AN: 67960

Other (OTH) AF: 0.411 AC: 867 AN: 2108

Alfa AF: 0.441 Hom.: 2489

Bravo AF: 0.383

Asia WGS AF: 0.416 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.0
DANN	Benign	0.63
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10773343; hg19: chr12-127428488;