chr4-71754414-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000583.4(GC):​c.1259A>T​(p.Lys420Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000155 in 1,292,838 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000015 ( 0 hom. )

Consequence

GC
NM_000583.4 missense

Scores

1
10
8

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.83
Variant links:
Genes affected
GC (HGNC:4187): (GC vitamin D binding protein) The protein encoded by this gene belongs to the albumin gene family. It is a multifunctional protein found in plasma, ascitic fluid, cerebrospinal fluid and on the surface of many cell types. It binds to vitamin D and its plasma metabolites and transports them to target tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GCNM_000583.4 linkuse as main transcriptc.1259A>T p.Lys420Ile missense_variant 10/13 ENST00000273951.13
GCNM_001204307.1 linkuse as main transcriptc.1316A>T p.Lys439Ile missense_variant 11/14
GCNM_001204306.1 linkuse as main transcriptc.1259A>T p.Lys420Ile missense_variant 11/14
GCXM_006714177.3 linkuse as main transcriptc.1259A>T p.Lys420Ile missense_variant 10/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GCENST00000273951.13 linkuse as main transcriptc.1259A>T p.Lys420Ile missense_variant 10/131 NM_000583.4 P1P02774-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000849
AC:
2
AN:
235700
Hom.:
0
AF XY:
0.00000784
AC XY:
1
AN XY:
127534
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000634
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000155
AC:
2
AN:
1292838
Hom.:
0
Cov.:
19
AF XY:
0.00000154
AC XY:
1
AN XY:
651282
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000483
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 17, 2021The c.1259A>T (p.K420I) alteration is located in exon 10 (coding exon 10) of the GC gene. This alteration results from a A to T substitution at nucleotide position 1259, causing the lysine (K) at amino acid position 420 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.39
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.22
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Benign
0.35
T;.;T
Eigen
Uncertain
0.67
Eigen_PC
Uncertain
0.64
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.81
T;T;T
M_CAP
Benign
0.016
T
MetaRNN
Uncertain
0.55
D;D;D
MetaSVM
Benign
-0.86
T
MutationAssessor
Uncertain
2.9
M;.;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.51
T
PROVEAN
Uncertain
-3.5
D;D;D
REVEL
Benign
0.27
Sift
Uncertain
0.0030
D;D;D
Sift4G
Pathogenic
0.0
D;D;D
Polyphen
1.0
.;.;D
Vest4
0.54
MutPred
0.64
Loss of disorder (P = 0.0018);.;Loss of disorder (P = 0.0018);
MVP
0.17
MPC
0.43
ClinPred
0.95
D
GERP RS
5.5
Varity_R
0.62
gMVP
0.63

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: rs1288936818; hg19: chr4-72620131; API