rs12409103

Variant names:

• chr1-31509081-G-A
• rs12409103
• ENST00000563550.5:n.1020G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-31509081-G-A
• chr1-31509081-G-C

Variant summary

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

The ENST00000563550.5(LDC1P):​n.1020G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,264 control chromosomes in the GnomAD database, including 22,448 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 0.54 (22417 hom., cov: 32)
  • Exomes 𝑓: 0.50 (31 hom.)
• Consequence: LDC1P ENST00000563550.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.33

Genes affected

LDC1P (HGNC:49677): (leucine decarboxylase 1, pseudogene)

LINC01226 (HGNC:49678): (long intergenic non-protein coding RNA 1226)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDC1P	ENST00000563550.5	n.1020G>A		non_coding_transcript_exon_variant	Exon 8 of 9	6
LINC01226	ENST00000639741.1	n.126+2675G>A		intron_variant	Intron 1 of 2	4
LINC01226	ENST00000639839.1	n.236+1731G>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81957 AN: 151900 Hom.: 22406 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.500 AC: 123 AN: 246 Hom.: 31 Cov.: 0 AF XY: 0.461 AC XY: 82 AN XY: 178

Gnomad4 AFR exome AF: 0.438

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.542

Gnomad4 NFE exome AF: 0.524

Gnomad4 OTH exome AF: 0.364

GnomAD4 genome AF: 0.539 AC: 82004 AN: 152018 Hom.: 22417 Cov.: 32 AF XY: 0.532 AC XY: 39556 AN XY: 74302

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.541

Alfa AF: 0.543 Hom.: 4563

Bravo AF: 0.543

Asia WGS AF: 0.452 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.097
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12409103; hg19: chr1-31974682;