rs7552206

Positions:

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

Variant summary

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

The XR_001736964.3(LYPLAL1):​n.28055-7250C>A 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 0.342 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: LYPLAL1 XR_001736964.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462

Genes affected

LYPLAL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LYPLAL1	XR_001736964.3	n.28055-7250C>A		intron_variant, non_coding_transcript_variant
LYPLAL1	XR_001736967.3	n.1056+78248C>A		intron_variant, non_coding_transcript_variant
LYPLAL1	XR_001736968.3	n.1009-7250C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.408

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7552206; hg19: chr1-219492898;