Variant rs10455872 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_005577.4(LPA):c.3947+467T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0425 in 152134 control chromosomes in the gnomAD Genomes database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.043 ( 192 hom., cov: 33)

Consequence

LPA
NM_005577.4 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.08

Links

LPA (HGNC:6667):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 6-160589086-A-G is Benign according to our data. Variant chr6-160589086-A-G is described in ClinVar as [Benign]. Clinvar id is 225938. Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPA	NM_005577.4 linkuse as main transcript	c.3947+467T>C		intron_variant		ENST00000316300.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPA	ENST00000316300.10 linkuse as main transcript	c.3947+467T>C		intron_variant		1	NM_005577.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0425

AC:

6468

AN:

152134

Hom.:

192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0122

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.0385

Gnomad ASJ

AF:

0.0300

Gnomad EAS

AF:

0.000967

Gnomad SAS

AF:

0.0105

Gnomad FIN

AF:

0.0354

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0695

Gnomad OTH

AF:

0.0436

Alfa

AF:

0.0616

Hom.:

414

Bravo

AF:

0.0411

Asia WGS

AF:

0.00636

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

LIPOPROTEIN(a) POLYMORPHISM

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Aug 07, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

Cadd

Benign

0.011

Dann

Benign

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over