Genetic Variant GPANK1:c.*90T>C (chr6-31662176-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033177.4(GPANK1):c.*90T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 806,402 control chromosomes in the GnomAD database, including 41,672 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 11812 hom., cov: 32)

Exomes 𝑓: 0.29 ( 29860 hom. )

Consequence

GPANK1
NM_033177.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.108

Publications

37 publications found

Variant links:

Genes affected

GPANK1 (HGNC:13920): (G-patch domain and ankyrin repeats 1) This gene is located in a cluster of HLA-B-associated transcripts, which is included in the human major histocompatability complex III region. This gene encodes a protein which is thought to play a role in immunity. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Nov 2010]

GPANK1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033177.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GPANK1	NM_033177.4	MANE Select	c.*90T>C	3_prime_UTR	Exon 3 of 3	NP_149417.1
GPANK1	NM_001199237.1		c.*90T>C	3_prime_UTR	Exon 4 of 4	NP_001186166.1
GPANK1	NM_001199238.1		c.*90T>C	3_prime_UTR	Exon 4 of 4	NP_001186167.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GPANK1	ENST00000375896.9	TSL:1 MANE Select	c.*90T>C	3_prime_UTR	Exon 3 of 3	ENSP00000365060.4
GPANK1	ENST00000375893.6	TSL:5	c.*90T>C	3_prime_UTR	Exon 4 of 4	ENSP00000365057.2
GPANK1	ENST00000375895.6	TSL:5	c.*90T>C	3_prime_UTR	Exon 4 of 4	ENSP00000365059.2

Frequencies

GnomAD3 genomes

AF:

0.376

AC:

57076

AN:

151942

Hom.:

11797

Cov.:

show subpopulations

Gnomad AFR

AF:

0.553

Gnomad AMI

AF:

0.261

Gnomad AMR

AF:

0.392

Gnomad ASJ

AF:

0.297

Gnomad EAS

AF:

0.383

Gnomad SAS

AF:

0.311

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.382

GnomAD4 exome

AF:

0.291

AC:

190359

AN:

654342

Hom.:

29860

Cov.:

AF XY:

0.286

AC XY:

96846

AN XY:

338140

show subpopulations

African (AFR)

AF:

0.553

AC:

8820

AN:

15952

American (AMR)

AF:

0.400

AC:

9292

AN:

23206

Ashkenazi Jewish (ASJ)

AF:

0.299

AC:

4303

AN:

14410

East Asian (EAS)

AF:

0.412

AC:

13333

AN:

32376

South Asian (SAS)

AF:

0.282

AC:

13601

AN:

48300

European-Finnish (FIN)

AF:

0.397

AC:

18682

AN:

47096

Middle Eastern (MID)

AF:

0.361

AC:

1363

AN:

3778

European-Non Finnish (NFE)

AF:

0.254

AC:

111261

AN:

437258

Other (OTH)

AF:

0.304

AC:

9704

AN:

31966

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

7351

14702

22054

29405

36756

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2538

5076

7614

10152

12690

<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:

0.376

AC:

57134

AN:

152060

Hom.:

11812

Cov.:

AF XY:

0.382

AC XY:

28384

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.553

AC:

22923

AN:

41474

American (AMR)

AF:

0.393

AC:

6008

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.297

AC:

1028

AN:

3466

East Asian (EAS)

AF:

0.383

AC:

1978

AN:

5170

South Asian (SAS)

AF:

0.311

AC:

1500

AN:

4822

European-Finnish (FIN)

AF:

0.420

AC:

4434

AN:

10568

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.266

AC:

18100

AN:

67954

Other (OTH)

AF:

0.381

AC:

805

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1730

3461

5191

6922

8652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.301

Hom.:

28954

Bravo

AF:

0.385

Asia WGS

AF:

0.358

AC:

1241

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.1

(source)

DANN

Benign

0.62

PhyloP100

0.11

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over