Genetic Variant NM_000583.4:c.1035-49_1035-42dupAATAAATA (chr4-71755148-C-CTATTTATT) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The NM_000583.4(GC):c.1035-49_1035-42dupAATAAATA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.60 ( 29258 hom., cov: 0)

Exomes 𝑓: 0.67 ( 74686 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: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GC	NM_000583.4 link	c.1035-49_1035-42dupAATAAATA	intron_variant	Intron 8 of 12	ENST00000273951.13	NP_000574.2	P02774-1
GC	NM_001204307.1 link	c.1092-49_1092-42dupAATAAATA	intron_variant	Intron 9 of 13		NP_001191236.1	P02774-3
GC	NM_001204306.1 link	c.1035-49_1035-42dupAATAAATA	intron_variant	Intron 9 of 13		NP_001191235.1	P02774-1
GC	NM_001440458.1 link	c.1035-49_1035-42dupAATAAATA	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.1035-49_1035-42dupAATAAATA		intron_variant	Intron 8 of 12	1	NM_000583.4	ENSP00000273951.8		P02774-1

Frequencies

GnomAD3 genomes

AF:

0.605

AC:

87662

AN:

144930

Hom.:

29250

Cov.:

show subpopulations

Gnomad AFR

AF:

0.315

Gnomad AMI

AF:

0.685

Gnomad AMR

AF:

0.654

Gnomad ASJ

AF:

0.794

Gnomad EAS

AF:

0.525

Gnomad SAS

AF:

0.791

Gnomad FIN

AF:

0.803

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.720

Gnomad OTH

AF:

0.617

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.667

AC:

189259

AN:

283546

Hom.:

74686

Cov.:

AF XY:

0.661

AC XY:

103969

AN XY:

157408

show subpopulations

African (AFR)

AF:

0.190

AC:

1426

AN:

7510

American (AMR)

AF:

0.312

AC:

2829

AN:

9056

Ashkenazi Jewish (ASJ)

AF:

0.723

AC:

4963

AN:

6868

East Asian (EAS)

AF:

0.352

AC:

3560

AN:

10102

South Asian (SAS)

AF:

0.649

AC:

10766

AN:

16594

European-Finnish (FIN)

AF:

0.647

AC:

14816

AN:

22902

Middle Eastern (MID)

AF:

0.497

AC:

950

AN:

1910

European-Non Finnish (NFE)

AF:

0.725

AC:

142772

AN:

196970

Other (OTH)

AF:

0.617

AC:

7177

AN:

11634

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.551

Heterozygous variant carriers

1709

3419

5128

6838

8547

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.605

AC:

87695

AN:

145018

Hom.:

29258

Cov.:

AF XY:

0.611

AC XY:

42921

AN XY:

70202

show subpopulations

African (AFR)

AF:

0.315

AC:

12345

AN:

39164

American (AMR)

AF:

0.654

AC:

9418

AN:

14392

Ashkenazi Jewish (ASJ)

AF:

0.794

AC:

2713

AN:

3418

East Asian (EAS)

AF:

0.525

AC:

2575

AN:

4904

South Asian (SAS)

AF:

0.794

AC:

3516

AN:

4430

European-Finnish (FIN)

AF:

0.803

AC:

7136

AN:

8884

Middle Eastern (MID)

AF:

0.656

AC:

189

AN:

288

European-Non Finnish (NFE)

AF:

0.720

AC:

47952

AN:

66636

Other (OTH)

AF:

0.617

AC:

1239

AN:

2008

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1340

2681

4021

5362

6702

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.707

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.1035-49_1035-42dupAATAAATA

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