rs1147270

Variant names:

• chr12-127000191-G-C
• rs1147270
• ENST00000512624.6:n.606+365C>G

Variant summary

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

The ENST00000512624.6(LINC02405):​n.606+365C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,772 control chromosomes in the GnomAD database, including 7,204 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 0.28 (7204 hom., cov: 31)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02405	NR_104646.1	n.606+365C>G		intron_variant	Intron 3 of 6
LOC105370063	XR_007063518.1	n.1410+2912G>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02405	ENST00000512624.6	n.606+365C>G		intron_variant	Intron 3 of 6	1
LINC02405	ENST00000540244.6	n.578+365C>G		intron_variant	Intron 3 of 3	3
LINC02405	ENST00000651439.2	n.560+365C>G		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41875 AN: 151656 Hom.: 7178 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.276 AC: 41958 AN: 151772 Hom.: 7204 Cov.: 31 AF XY: 0.281 AC XY: 20834 AN XY: 74146

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.263

Alfa AF: 0.224 Hom.: 573

Bravo AF: 0.308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1147270; hg19: chr12-127484736;