rs12409103

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDC1P	ENST00000563550.5	n.1020G>A		non_coding_transcript_exon_variant	8/9
LINC01226	ENST00000639741.1	n.126+2675G>A		intron_variant, non_coding_transcript_variant		4
LINC01226	ENST00000640157.1	n.122+2675G>A		intron_variant, non_coding_transcript_variant		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;