Variant 17-4168008-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001330063.2(ANKFY1):c.3378-97C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 1,388,312 control chromosomes in the GnomAD database, including 252,458 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 25407 hom., cov: 33)

Exomes 𝑓: 0.60 ( 227051 hom. )

Consequence

ANKFY1
NM_001330063.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.30

Variant links:

Genes affected

ANKFY1 (HGNC:20763): (ankyrin repeat and FYVE domain containing 1) This gene encodes a cytoplasmic protein that contains a coiled-coil structure and a BTB/POZ domain at its N-terminus, ankyrin repeats in the middle portion, and a FYVE-finger motif at its C-terminus. This protein belongs to a subgroup of double zinc finger proteins which may be involved in vesicle or protein transport. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, Apr 2012]

ANKFY1 links:

CYB5D2 (HGNC:28471): (cytochrome b5 domain containing 2) Predicted to enable heme binding activity. Predicted to be involved in nervous system development. Predicted to act upstream of or within positive regulation of neuron differentiation. Predicted to be located in extracellular region. Predicted to be active in endomembrane system and membrane. [provided by Alliance of Genome Resources, Apr 2022]

CYB5D2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 17-4168008-G-C is Benign according to our data. Variant chr17-4168008-G-C is described in ClinVar as [Benign]. Clinvar id is 1229739.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKFY1	NM_001330063.2 link	c.3378-97C>G		intron_variant		ENST00000341657.9	NP_001316992.1	Q9P2R3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKFY1	ENST00000341657.9 link	c.3378-97C>G		intron_variant		5	NM_001330063.2	ENSP00000343362.4		Q9P2R3-1

Frequencies

GnomAD3 genomes

AF:

0.576

AC:

87342

AN:

151718

Hom.:

25402

Cov.:

show subpopulations

Gnomad AFR

AF:

0.498

Gnomad AMI

AF:

0.514

Gnomad AMR

AF:

0.559

Gnomad ASJ

AF:

0.594

Gnomad EAS

AF:

0.763

Gnomad SAS

AF:

0.650

Gnomad FIN

AF:

0.593

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.604

Gnomad OTH

AF:

0.580

GnomAD4 exome

AF:

0.604

AC:

746846

AN:

1236476

Hom.:

227051

Cov.:

AF XY:

0.605

AC XY:

368560

AN XY:

609222

show subpopulations

Gnomad4 AFR exome

AF:

0.498

Gnomad4 AMR exome

AF:

0.556

Gnomad4 ASJ exome

AF:

0.597

Gnomad4 EAS exome

AF:

0.731

Gnomad4 SAS exome

AF:

0.641

Gnomad4 FIN exome

AF:

0.596

Gnomad4 NFE exome

AF:

0.601

Gnomad4 OTH exome

AF:

0.610

GnomAD4 genome

AF:

0.575

AC:

87367

AN:

151836

Hom.:

25407

Cov.:

AF XY:

0.578

AC XY:

42889

AN XY:

74168

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.558

Gnomad4 ASJ

AF:

0.594

Gnomad4 EAS

AF:

0.763

Gnomad4 SAS

AF:

0.650

Gnomad4 FIN

AF:

0.593

Gnomad4 NFE

AF:

0.604

Gnomad4 OTH

AF:

0.577

Alfa

AF:

0.466

Hom.:

1321

Bravo

AF:

0.569

Asia WGS

AF:

0.670

AC:

2329

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.6

DANN

Benign

0.71

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over