Variant chr17-4169413-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001330063.2(ANKFY1):c.3287-125C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0243 in 696,926 control chromosomes in the GnomAD database, including 579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.047 ( 355 hom., cov: 32)

Exomes 𝑓: 0.018 ( 224 hom. )

Consequence

ANKFY1
NM_001330063.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.176

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 17-4169413-G-A is Benign according to our data. Variant chr17-4169413-G-A is described in ClinVar as [Benign]. Clinvar id is 1259674.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 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.3287-125C>T		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.3287-125C>T		intron_variant		5	NM_001330063.2	ENSP00000343362	P3	Q9P2R3-1

Frequencies

GnomAD3 genomes

AF:

0.0468

AC:

7120

AN:

152176

Hom.:

353

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0336

Gnomad ASJ

AF:

0.0190

Gnomad EAS

AF:

0.0138

Gnomad SAS

AF:

0.00455

Gnomad FIN

AF:

0.0198

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0150

Gnomad OTH

AF:

0.0330

GnomAD4 exome

AF:

0.0180

AC:

9817

AN:

544632

Hom.:

224

AF XY:

0.0170

AC XY:

4811

AN XY:

283170

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.0210

Gnomad4 ASJ exome

AF:

0.0177

Gnomad4 EAS exome

AF:

0.00667

Gnomad4 SAS exome

AF:

0.00449

Gnomad4 FIN exome

AF:

0.0208

Gnomad4 NFE exome

AF:

0.0147

Gnomad4 OTH exome

AF:

0.0288

GnomAD4 genome

AF:

0.0468

AC:

7133

AN:

152294

Hom.:

355

Cov.:

AF XY:

0.0463

AC XY:

3445

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.124

Gnomad4 AMR

AF:

0.0336

Gnomad4 ASJ

AF:

0.0190

Gnomad4 EAS

AF:

0.0135

Gnomad4 SAS

AF:

0.00414

Gnomad4 FIN

AF:

0.0198

Gnomad4 NFE

AF:

0.0150

Gnomad4 OTH

AF:

0.0332

Alfa

AF:

0.0130

Hom.:

Bravo

AF:

0.0517

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.9

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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