rs17725531

Positions:

• chr19-43822026-T-G

Variant summary

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

The ENST00000602179.1(LYPD5):​c.-66+4973A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,192 control chromosomes in the GnomAD database, including 2,028 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 0.16 (2028 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LYPD5 ENST00000602179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.980

Genes affected

LYPD5 (HGNC:26397): (LY6/PLAUR domain containing 5) Predicted to be located in extracellular region. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LYPD5	ENST00000602179.1	c.-66+4973A>C		intron_variant		4		ENSP00000471909
LYPD5	ENST00000599397.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23615 AN: 152074 Hom.: 2018 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.190

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.156 AC: 23669 AN: 152192 Hom.: 2028 Cov.: 32 AF XY: 0.153 AC XY: 11385 AN XY: 74428

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.0768

Gnomad4 FIN AF: 0.0767

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.192

Alfa AF: 0.139 Hom.: 434

Bravo AF: 0.171

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.2
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17725531; hg19: chr19-44326178;