rs1147270

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-1.04).
• 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	ENST00000755438.1	n.988C>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02405	ENST00000540244.7	n.776+365C>G		intron_variant	Intron 3 of 3	3

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

African (AFR) AF: 0.420 AC: 17366 AN: 41354

American (AMR) AF: 0.414 AC: 6305 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3466

East Asian (EAS) AF: 0.558 AC: 2836 AN: 5078

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4816

European-Finnish (FIN) AF: 0.187 AC: 1980 AN: 10572

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11083 AN: 67938

Other (OTH) AF: 0.263 AC: 555 AN: 2114

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
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1147270; hg19: chr12-127484736;