Genetic Variant GPANK1:c.*544T>C (chr6-31661722-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.*544T>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 0.0674 in 167,066 control chromosomes in the GnomAD database, including 534 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 0.067 ( 477 hom., cov: 32)

Exomes 𝑓: 0.071 ( 57 hom. )

Consequence

GPANK1
NM_033177.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.132

Publications

17 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPANK1	NM_033177.4 link	c.*544T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000375896.9	NP_149417.1	O95872A0A024RCU2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPANK1	ENST00000375896.9 link	c.*544T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_033177.4	ENSP00000365060.4		O95872
GPANK1	ENST00000375906.5 link	c.*544T>C		3_prime_UTR_variant	Exon 4 of 4	2		ENSP00000365071.1		O95872

Frequencies

GnomAD3 genomes

AF:

0.0672

AC:

10217

AN:

152082

Hom.:

476

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0190

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0631

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.0183

Gnomad SAS

AF:

0.0367

Gnomad FIN

AF:

0.0670

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0981

Gnomad OTH

AF:

0.0738

GnomAD4 exome

AF:

0.0707

AC:

1052

AN:

14870

Hom.:

Cov.:

AF XY:

0.0688

AC XY:

710

AN XY:

10324

show subpopulations

African (AFR)

AF:

0.0240

AC:

AN:

208

American (AMR)

AF:

0.0186

AC:

AN:

322

Ashkenazi Jewish (ASJ)

AF:

0.152

AC:

AN:

178

East Asian (EAS)

AF:

0.0537

AC:

AN:

354

South Asian (SAS)

AF:

0.0335

AC:

114

AN:

3408

European-Finnish (FIN)

AF:

0.0579

AC:

AN:

432

Middle Eastern (MID)

AF:

0.0909

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0882

AC:

822

AN:

9318

Other (OTH)

AF:

0.0495

AC:

AN:

606

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

107

143

179

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0671

AC:

10213

AN:

152196

Hom.:

477

Cov.:

AF XY:

0.0655

AC XY:

4876

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.0190

AC:

787

AN:

41530

American (AMR)

AF:

0.0630

AC:

964

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

495

AN:

3470

East Asian (EAS)

AF:

0.0183

AC:

AN:

5188

South Asian (SAS)

AF:

0.0367

AC:

177

AN:

4822

European-Finnish (FIN)

AF:

0.0670

AC:

710

AN:

10590

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0981

AC:

6673

AN:

67992

Other (OTH)

AF:

0.0735

AC:

155

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

490

981

1471

1962

2452

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0855

Hom.:

1450

Bravo

AF:

0.0651

Asia WGS

AF:

0.0290

AC:

103

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.4

(source)

DANN

Benign

0.60

PhyloP100

0.13

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over