dbSNP rs17725531: LYPD5:c.-66+4973A>C (chr19-43822026-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.980

Publications

5 publications found

Variant links:

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]

LYPD5 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPD5	ENST00000602179.1 link	c.-66+4973A>C		intron_variant	Intron 1 of 3	4		ENSP00000471909.1		M0R1J4
LYPD5	ENST00000599397.1 link	n.*31A>C		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23615

AN:

152074

Hom.:

2018

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.156

AC:

23669

AN:

152192

Hom.:

2028

Cov.:

AF XY:

0.153

AC XY:

11385

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.211

AC:

8766

AN:

41500

American (AMR)

AF:

0.181

AC:

2763

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

388

AN:

3468

East Asian (EAS)

AF:

0.251

AC:

1299

AN:

5178

South Asian (SAS)

AF:

0.0768

AC:

371

AN:

4828

European-Finnish (FIN)

AF:

0.0767

AC:

814

AN:

10606

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8693

AN:

68010

Other (OTH)

AF:

0.192

AC:

406

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1009

2018

3026

4035

5044

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.146

Hom.:

1077

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

(source)

DANN

Benign

0.89

PhyloP100

0.98

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over