rs7552206

Variant names:

• chr1-219319556-C-A
• rs7552206
• ENST00000811384.1:n.291+4378G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-219319556-C-A
• chr1-219319556-C-G

Variant summary

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

The ENST00000811384.1(ENSG00000305505):​n.291+4378G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,960 control chromosomes in the GnomAD database, including 9,789 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 0.34 (9789 hom., cov: 31)
• Consequence: ENSG00000305505 ENST00000811384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1	XR_001736964.3	n.28055-7250C>A		intron_variant	Intron 10 of 10
LYPLAL1	XR_001736967.3	n.1056+78248C>A		intron_variant	Intron 7 of 9
LYPLAL1	XR_001736968.3	n.1009-7250C>A		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305505	ENST00000811384.1	n.291+4378G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51965 AN: 151844 Hom.: 9763 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.342 AC: 52032 AN: 151960 Hom.: 9789 Cov.: 31 AF XY: 0.350 AC XY: 26025 AN XY: 74276

African (AFR) AF: 0.311 AC: 12890 AN: 41442

American (AMR) AF: 0.401 AC: 6119 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3468

East Asian (EAS) AF: 0.809 AC: 4166 AN: 5148

South Asian (SAS) AF: 0.545 AC: 2624 AN: 4812

European-Finnish (FIN) AF: 0.287 AC: 3031 AN: 10570

Middle Eastern (MID) AF: 0.486 AC: 141 AN: 290

European-Non Finnish (NFE) AF: 0.303 AC: 20559 AN: 67954

Other (OTH) AF: 0.408 AC: 859 AN: 2106

Alfa AF: 0.191 Hom.: 415

Bravo AF: 0.350

Asia WGS AF: 0.656 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs7552206; hg19: chr1-219492898;