chr1-219149936-T-C

Variant names:

• chr1-219149936-T-C
• rs12079503
• ENST00000441331.2:n.452+3A>G

Variant summary

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

The ENST00000441331.2(LYPLAL1-DT):​n.452+3A>G variant causes a splice region, intron 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 ENST00000441331.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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	ENST00000441331.2	n.452+3A>G		splice_region_variant, intron_variant	Intron 3 of 3	3
LYPLAL1-DT	ENST00000654859.2	n.431+6184A>G		intron_variant	Intron 2 of 3
LYPLAL1-DT	ENST00000655283.1	n.463+3A>G		splice_region_variant, intron_variant	Intron 3 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

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

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

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0971

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.134

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12079503; hg19: chr1-219323278;