rs12043736

chr1-219304811-A-G

Variant summary

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

The XR_001736964.3(LYPLAL1):n.28054+9660A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,038 control chromosomes in the GnomAD database, including 9,745 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 0.35 (9745 hom., cov: 32)
• Consequence: LYPLAL1 XR_001736964.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

LYPLAL1 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYPLAL1	XR_001736964.3	n.28054+9660A>G		intron_variant, non_coding_transcript_variant
LYPLAL1	XR_001736967.3	n.1056+63503A>G		intron_variant, non_coding_transcript_variant
LYPLAL1	XR_001736968.3	n.1009-21995A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53534 AN: 151920 Hom.: 9746 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.341

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.352 AC: 53549 AN: 152038 Hom.: 9745 Cov.: 32 AF XY: 0.348 AC XY: 25898 AN XY: 74314

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.338

Alfa AF: 0.372 Hom.: 1845

Bravo AF: 0.353

Asia WGS AF: 0.207 AC: 724 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	7.8
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12043736; hg19: chr1-219478153; COSMIC: COSV60028872;