rs12043736

Variant names:

• chr1-219304811-A-G
• rs12043736
• ENST00000811384.1:n.292-10822T>C

Variant summary

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

The ENST00000811384.1(ENSG00000305505):​n.292-10822T>C variant causes a intron 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: ENSG00000305505 ENST00000811384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 2 publications found

Genes affected

ENSG00000305505 (HGNC:):

LYPLAL1 (HGNC:20440): (lysophospholipase like 1) Predicted to enable carboxylic ester hydrolase activity and palmitoyl-(protein) hydrolase activity. Predicted to be involved in protein depalmitoylation. Predicted to act upstream of or within negative regulation of Golgi to plasma membrane protein transport. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811384.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305505	ENST00000811384.1		n.292-10822T>C		intron	N/A

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

African (AFR) AF: 0.294 AC: 12201 AN: 41472

American (AMR) AF: 0.392 AC: 5991 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3470

East Asian (EAS) AF: 0.163 AC: 841 AN: 5172

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4822

European-Finnish (FIN) AF: 0.416 AC: 4391 AN: 10552

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26803 AN: 67956

Other (OTH) AF: 0.338 AC: 713 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.8
DANN	Benign	0.66
PhyloP100		-0.057

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12043736;

hg19: chr1-219478153;

COSMIC: COSV60028872;