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rs76587671

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_000477.7(ALB):c.1759G>A(p.Asp587Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 780,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as other (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D587G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

ALB
NM_000477.7 missense

Scores

19

Clinical Significance

other no assertion criteria provided O:1

Conservation

PhyloP100: -0.0840
Variant links:
Genes affected
ALB (HGNC:399): (albumin) This gene encodes the most abundant protein in human blood. This protein functions in the regulation of blood plasma colloid osmotic pressure and acts as a carrier protein for a wide range of endogenous molecules including hormones, fatty acids, and metabolites, as well as exogenous drugs. Additionally, this protein exhibits an esterase-like activity with broad substrate specificity. The encoded preproprotein is proteolytically processed to generate the mature protein. A peptide derived from this protein, EPI-X4, is an endogenous inhibitor of the CXCR4 chemokine receptor. [provided by RefSeq, Jul 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.14955488).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ALBNM_000477.7 linkuse as main transcriptc.1759G>A p.Asp587Asn missense_variant 13/15 ENST00000295897.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ALBENST00000295897.9 linkuse as main transcriptc.1759G>A p.Asp587Asn missense_variant 13/151 NM_000477.7 P1P02768-1

Frequencies

GnomAD3 genomes
AF:
0.0000592
AC:
9
AN:
152108
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000328
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000199
AC:
5
AN:
251330
Hom.:
0
AF XY:
0.0000221
AC XY:
3
AN XY:
135828
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.0000868
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000111
AC:
7
AN:
628670
Hom.:
0
Cov.:
34
AF XY:
0.0000117
AC XY:
4
AN XY:
342484
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000915
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000143
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000571
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000592
AC:
9
AN:
152108
Hom.:
0
Cov.:
32
AF XY:
0.0000538
AC XY:
4
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.0000483
Gnomad4 AMR
AF:
0.000328
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000282
Hom.:
0
Bravo
AF:
0.0000529

ClinVar

Significance: other
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

ALBUMIN FUKUOKA 1 Other:1
other, no assertion criteria providedliterature onlyOMIMJul 18, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.091
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.40
Cadd
Benign
12
Dann
Benign
0.87
DEOGEN2
Benign
0.23
T;.;.;.;.;.;T
Eigen
Benign
-0.72
Eigen_PC
Benign
-0.80
FATHMM_MKL
Benign
0.20
N
LIST_S2
Benign
0.78
T;T;T;T;T;T;T
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.15
T;T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.85
L;.;.;.;.;.;.
MutationTaster
Benign
1.0
N;N;N;N;N
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-1.6
N;.;.;N;N;N;N
REVEL
Benign
0.12
Sift
Benign
0.34
T;.;.;T;T;T;T
Sift4G
Benign
0.28
T;T;T;T;T;T;T
Polyphen
0.0090
B;.;.;B;B;.;B
Vest4
0.17
MutPred
0.49
Loss of ubiquitination at K584 (P = 0.0853);.;.;.;.;Loss of ubiquitination at K584 (P = 0.0853);.;
MVP
0.61
MPC
0.21
ClinPred
0.029
T
GERP RS
1.5
Varity_R
0.29
gMVP
0.24

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: rs76587671; hg19: chr4-74285330; COSMIC: COSV55739624; COSMIC: COSV55739624; API