12-126983603-T-C

Position:

• chr12-126983603-T-C

Variant summary

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

The NR_104646.1(LINC02405):​n.607-7686A>G 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 0.0835 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 NR_104646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

Genes affected

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

LOC105370063 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02405	NR_104646.1	n.607-7686A>G		intron_variant, non_coding_transcript_variant
LOC105370063	XR_007063518.1	n.1308+2299T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02405	ENST00000662160.1	n.700-7686A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.0346

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0286

Gnomad4 FIN AF: 0.00235

Gnomad4 NFE AF: 0.00567

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0400 Hom.: 133

Bravo AF: 0.0964

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1147262; hg19: chr12-127468148;