Genetic Variant NM_000583.4:c.1035-57_1035-42dupAATAAATAAATAAATA (chr4-71755148-C-CTATTTATTTATTTATT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000583.4(GC):c.1035-57_1035-42dupAATAAATAAATAAATA 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 0.11 ( 942 hom., cov: 0)

Exomes 𝑓: 0.059 ( 1162 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]

GC links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GC	NM_000583.4 link	c.1035-57_1035-42dupAATAAATAAATAAATA	intron_variant	Intron 8 of 12	ENST00000273951.13	NP_000574.2	P02774-1
GC	NM_001204307.1 link	c.1092-57_1092-42dupAATAAATAAATAAATA	intron_variant	Intron 9 of 13		NP_001191236.1	P02774-3
GC	NM_001204306.1 link	c.1035-57_1035-42dupAATAAATAAATAAATA	intron_variant	Intron 9 of 13		NP_001191235.1	P02774-1
GC	NM_001440458.1 link	c.1035-57_1035-42dupAATAAATAAATAAATA	intron_variant	Intron 8 of 11		NP_001427387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GC	ENST00000273951.13 link	c.1035-57_1035-42dupAATAAATAAATAAATA		intron_variant	Intron 8 of 12	1	NM_000583.4	ENSP00000273951.8		P02774-1

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

15512

AN:

145004

Hom.:

942

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.0638

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.0542

Gnomad EAS

AF:

0.0436

Gnomad SAS

AF:

0.0615

Gnomad FIN

AF:

0.0380

Gnomad MID

AF:

0.148

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.115

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0590

AC:

16725

AN:

283692

Hom.:

1162

Cov.:

AF XY:

0.0609

AC XY:

9597

AN XY:

157458

show subpopulations

African (AFR)

AF:

0.0526

AC:

395

AN:

7514

American (AMR)

AF:

0.0332

AC:

301

AN:

9062

Ashkenazi Jewish (ASJ)

AF:

0.0393

AC:

270

AN:

6868

East Asian (EAS)

AF:

0.0196

AC:

199

AN:

10134

South Asian (SAS)

AF:

0.0401

AC:

666

AN:

16628

European-Finnish (FIN)

AF:

0.0392

AC:

900

AN:

22948

Middle Eastern (MID)

AF:

0.0480

AC:

AN:

1916

European-Non Finnish (NFE)

AF:

0.0670

AC:

13197

AN:

196974

Other (OTH)

AF:

0.0605

AC:

705

AN:

11648

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

629

1258

1886

2515

3144

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.107

AC:

15511

AN:

145092

Hom.:

942

Cov.:

AF XY:

0.101

AC XY:

7100

AN XY:

70238

show subpopulations

African (AFR)

AF:

0.116

AC:

4551

AN:

39204

American (AMR)

AF:

0.100

AC:

1443

AN:

14392

Ashkenazi Jewish (ASJ)

AF:

0.0542

AC:

185

AN:

3416

East Asian (EAS)

AF:

0.0435

AC:

214

AN:

4914

South Asian (SAS)

AF:

0.0607

AC:

269

AN:

4430

European-Finnish (FIN)

AF:

0.0380

AC:

338

AN:

8898

Middle Eastern (MID)

AF:

0.149

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.123

AC:

8180

AN:

66644

Other (OTH)

AF:

0.115

AC:

231

AN:

2012

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

623

1246

1868

2491

3114

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0652

Hom.:

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)

(source)

Splicing

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

Publications

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NM_000583.4:c.1035-57_1035-42dupAATAAATAAATAAATA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over