chr4-71755148-C-CTATTTATTTATT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000583.4(GC):​c.1035-53_1035-42dupAATAAATAAATA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 1864 hom., cov: 0)
Exomes 𝑓: 0.078 ( 1902 hom. )
Failed GnomAD Quality Control

Consequence

GC
NM_000583.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.440

Publications

0 publications found
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 was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GCNM_000583.4 linkc.1035-53_1035-42dupAATAAATAAATA intron_variant Intron 8 of 12 ENST00000273951.13 NP_000574.2 P02774-1
GCNM_001204307.1 linkc.1092-53_1092-42dupAATAAATAAATA intron_variant Intron 9 of 13 NP_001191236.1 P02774-3
GCNM_001204306.1 linkc.1035-53_1035-42dupAATAAATAAATA intron_variant Intron 9 of 13 NP_001191235.1 P02774-1
GCNM_001440458.1 linkc.1035-53_1035-42dupAATAAATAAATA intron_variant Intron 8 of 11 NP_001427387.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GCENST00000273951.13 linkc.1035-53_1035-42dupAATAAATAAATA intron_variant Intron 8 of 12 1 NM_000583.4 ENSP00000273951.8 P02774-1

Frequencies

GnomAD3 genomes
AF:
0.149
AC:
21625
AN:
144960
Hom.:
1860
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.199
Gnomad AMI
AF:
0.184
Gnomad AMR
AF:
0.146
Gnomad ASJ
AF:
0.0814
Gnomad EAS
AF:
0.333
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.0891
Gnomad MID
AF:
0.116
Gnomad NFE
AF:
0.120
Gnomad OTH
AF:
0.137
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0781
AC:
22110
AN:
283204
Hom.:
1902
Cov.:
9
AF XY:
0.0814
AC XY:
12793
AN XY:
157196
show subpopulations
African (AFR)
AF:
0.0898
AC:
674
AN:
7504
American (AMR)
AF:
0.0593
AC:
537
AN:
9054
Ashkenazi Jewish (ASJ)
AF:
0.0587
AC:
403
AN:
6862
East Asian (EAS)
AF:
0.177
AC:
1784
AN:
10106
South Asian (SAS)
AF:
0.0809
AC:
1342
AN:
16588
European-Finnish (FIN)
AF:
0.0676
AC:
1548
AN:
22904
Middle Eastern (MID)
AF:
0.0584
AC:
112
AN:
1918
European-Non Finnish (NFE)
AF:
0.0745
AC:
14642
AN:
196620
Other (OTH)
AF:
0.0917
AC:
1068
AN:
11648
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.473
Heterozygous variant carriers
0
816
1632
2448
3264
4080
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
322
644
966
1288
1610
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.149
AC:
21637
AN:
145048
Hom.:
1864
Cov.:
0
AF XY:
0.149
AC XY:
10466
AN XY:
70228
show subpopulations
African (AFR)
AF:
0.199
AC:
7785
AN:
39168
American (AMR)
AF:
0.146
AC:
2104
AN:
14396
Ashkenazi Jewish (ASJ)
AF:
0.0814
AC:
278
AN:
3416
East Asian (EAS)
AF:
0.333
AC:
1636
AN:
4908
South Asian (SAS)
AF:
0.126
AC:
560
AN:
4428
European-Finnish (FIN)
AF:
0.0891
AC:
793
AN:
8902
Middle Eastern (MID)
AF:
0.115
AC:
33
AN:
288
European-Non Finnish (NFE)
AF:
0.120
AC:
8007
AN:
66642
Other (OTH)
AF:
0.138
AC:
277
AN:
2010
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
850
1700
2550
3400
4250
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
242
484
726
968
1210
<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:
0.114
Hom.:
39

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.44
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs58603194; hg19: chr4-72620865; API