Variant chr17-4173320-C-T 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.3014+34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.075 in 1,600,352 control chromosomes in the GnomAD database, including 5,361 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.067 ( 448 hom., cov: 33)

Exomes 𝑓: 0.076 ( 4913 hom. )

Consequence

ANKFY1
NM_001330063.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.52

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 17-4173320-C-T is Benign according to our data. Variant chr17-4173320-C-T is described in ClinVar as [Benign]. Clinvar id is 1241236.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKFY1	NM_001330063.2 linkuse as main transcript	c.3014+34G>A		intron_variant		ENST00000341657.9	NP_001316992.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKFY1	ENST00000341657.9 linkuse as main transcript	c.3014+34G>A		intron_variant		5	NM_001330063.2	ENSP00000343362	P3	Q9P2R3-1

Frequencies

GnomAD3 genomes

AF:

0.0671

AC:

10217

AN:

152164

Hom.:

444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0255

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.0491

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.0782

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0710

Gnomad OTH

AF:

0.0641

GnomAD3 exomes

AF:

0.0914

AC:

22575

AN:

246878

Hom.:

1288

AF XY:

0.0926

AC XY:

12433

AN XY:

134302

show subpopulations

Gnomad AFR exome

AF:

0.0230

Gnomad AMR exome

AF:

0.159

Gnomad ASJ exome

AF:

0.109

Gnomad EAS exome

AF:

0.0511

Gnomad SAS exome

AF:

0.145

Gnomad FIN exome

AF:

0.0713

Gnomad NFE exome

AF:

0.0746

Gnomad OTH exome

AF:

0.0828

GnomAD4 exome

AF:

0.0758

AC:

109769

AN:

1448070

Hom.:

4913

Cov.:

AF XY:

0.0780

AC XY:

56266

AN XY:

721134

show subpopulations

Gnomad4 AFR exome

AF:

0.0241

Gnomad4 AMR exome

AF:

0.154

Gnomad4 ASJ exome

AF:

0.104

Gnomad4 EAS exome

AF:

0.0393

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.0733

Gnomad4 NFE exome

AF:

0.0696

Gnomad4 OTH exome

AF:

0.0755

GnomAD4 genome

AF:

0.0672

AC:

10233

AN:

152282

Hom.:

448

Cov.:

AF XY:

0.0691

AC XY:

5149

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.0255

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.106

Gnomad4 EAS

AF:

0.0490

Gnomad4 SAS

AF:

0.138

Gnomad4 FIN

AF:

0.0782

Gnomad4 NFE

AF:

0.0710

Gnomad4 OTH

AF:

0.0653

Alfa

AF:

0.0472

Hom.:

Bravo

AF:

0.0676

Asia WGS

AF:

0.104

AC:

362

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 11, 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

-0.91

CADD

Benign

0.056

DANN

Benign

0.90

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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