1-31509081-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563550.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LDC1P	ENST00000563550.5	TSL:6	n.1020G>A		non_coding_transcript_exon	Exon 8 of 9
	LINC01226	ENST00000639741.1	TSL:4	n.126+2675G>A		intron	N/A
	LINC01226	ENST00000639839.1	TSL:4	n.236+1731G>A		intron	N/A

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

African (AFR) AF: 0.438 AC: 7 AN: 16

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 3 AN: 6

East Asian (EAS) AF: 0.500 AC: 3 AN: 6

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.542 AC: 13 AN: 24

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.524 AC: 88 AN: 168

Other (OTH) AF: 0.364 AC: 8 AN: 22

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

African (AFR) AF: 0.601 AC: 24893 AN: 41446

American (AMR) AF: 0.460 AC: 7031 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1985 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2349 AN: 5154

South Asian (SAS) AF: 0.461 AC: 2221 AN: 4816

European-Finnish (FIN) AF: 0.478 AC: 5051 AN: 10566

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36726 AN: 67970

Other (OTH) AF: 0.541 AC: 1141 AN: 2108

Alfa AF: 0.544 Hom.: 4700

Bravo AF: 0.543

Asia WGS AF: 0.452 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.097
DANN	Benign	0.77
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs12409103; hg19: chr1-31974682;