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rs10455872

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

2

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.08

Links

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
LPANM_005577.4 linkuse as main transcriptc.3947+467T>C intron_variant ENST00000316300.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LPAENST00000316300.10 linkuse as main transcriptc.3947+467T>C intron_variant 1 NM_005577.4 P1

Frequencies

GnomAD3 genomes
AF:
0.0425
AC:
6468
AN:
152134
Hom.:
192
Cov.:
33
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:
23
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 providedliterature onlyOMIMAug 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.

Other links and lift over

dbSNP: rs10455872; hg19: chr6-161010118; COSMIC: COSV60310358;