rs12079503

Variant names:

• chr1-219149936-T-C
• rs12079503
• ENST00000811118.1:n.539A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-219149936-T-C
• chr1-219149936-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000811118.1(LYPLAL1-DT):​n.539A>G 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 0.137 in 152,080 control chromosomes in the GnomAD database, including 1,508 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 0.14 (1508 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: LYPLAL1-DT ENST00000811118.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 8 publications found

Genes affected

LYPLAL1-DT (HGNC:50560): (LYPLAL1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1-DT	NR_038845.1	n.492+3A>G		splice_region_variant, intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPLAL1-DT	ENST00000811118.1	n.539A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LYPLAL1-DT	ENST00000811119.1	n.417A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LYPLAL1-DT	ENST00000811120.1	n.629A>G		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20825 AN: 151952 Hom.: 1503 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0971

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.133

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.137 AC: 20843 AN: 152070 Hom.: 1508 Cov.: 32 AF XY: 0.137 AC XY: 10167 AN XY: 74328

African (AFR) AF: 0.161 AC: 6683 AN: 41474

American (AMR) AF: 0.145 AC: 2220 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1377 AN: 5162

South Asian (SAS) AF: 0.107 AC: 517 AN: 4816

European-Finnish (FIN) AF: 0.0971 AC: 1027 AN: 10578

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7984 AN: 67978

Other (OTH) AF: 0.134 AC: 284 AN: 2112

Alfa AF: 0.132 Hom.: 203

Bravo AF: 0.145

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.61
PhyloP100		0.072
Mutation Taster		=93/7	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12079503; hg19: chr1-219323278;