Variant rs7029 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPANK1	NM_033177.4 linkuse as main transcript	c.*90T>C		3_prime_UTR_variant	3/3	ENST00000375896.9	NP_149417.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPANK1	ENST00000375896.9 linkuse as main transcript	c.*90T>C		3_prime_UTR_variant	3/3	1	NM_033177.4	ENSP00000365060	P1

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

Gnomad4 AFR exome

AF:

0.553

Gnomad4 AMR exome

AF:

0.400

Gnomad4 ASJ exome

AF:

0.299

Gnomad4 EAS exome

AF:

0.412

Gnomad4 SAS exome

AF:

0.282

Gnomad4 FIN exome

AF:

0.397

Gnomad4 NFE exome

AF:

0.254

Gnomad4 OTH exome

AF:

0.304

GnomAD4 genome

AF:

0.376

AC:

57134

AN:

152060

Hom.:

11812

Cov.:

AF XY:

0.382

AC XY:

28384

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.553

Gnomad4 AMR

AF:

0.393

Gnomad4 ASJ

AF:

0.297

Gnomad4 EAS

AF:

0.383

Gnomad4 SAS

AF:

0.311

Gnomad4 FIN

AF:

0.420

Gnomad4 NFE

AF:

0.266

Gnomad4 OTH

AF:

0.381

Alfa

AF:

0.284

Hom.:

9460

Bravo

AF:

0.385

Asia WGS

AF:

0.358

AC:

1241

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.1

DANN

Benign

0.62

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over