12-126972412-C-T

Variant summary

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

The NR_104646.1(LINC02405):n.685+3427G>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 0.0971 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 NR_104646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02405	NR_104646.1	n.685+3427G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02405	ENST00000662160.1	n.778+3427G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0380

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.0365

Gnomad4 FIN AF: 0.00254

Gnomad4 NFE AF: 0.00603

Gnomad4 OTH AF: 0.0833

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1344361; hg19: chr12-127456957;