14-67790366-T-C

Variant summary

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

The NM_015346.4(ZFYVE26):​c.2755+206A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,100 control chromosomes in the GnomAD database, including 31,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.64 ( 31613 hom., cov: 32)

Consequence

ZFYVE26
NM_015346.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.38
Variant links:
Genes affected
ZFYVE26 (HGNC:20761): (zinc finger FYVE-type containing 26) This gene encodes a protein which contains a FYVE zinc finger binding domain. The presence of this domain is thought to target these proteins to membrane lipids through interaction with phospholipids in the membrane. Mutations in this gene are associated with autosomal recessive spastic paraplegia-15. [provided by RefSeq, Oct 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 14-67790366-T-C is Benign according to our data. Variant chr14-67790366-T-C is described in ClinVar as [Benign]. Clinvar id is 1245410.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZFYVE26NM_015346.4 linkc.2755+206A>G intron_variant Intron 15 of 41 ENST00000347230.9 NP_056161.2 Q68DK2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZFYVE26ENST00000347230.9 linkc.2755+206A>G intron_variant Intron 15 of 41 1 NM_015346.4 ENSP00000251119.5 Q68DK2-1

Frequencies

GnomAD3 genomes
AF:
0.639
AC:
97071
AN:
151982
Hom.:
31588
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.563
Gnomad AMI
AF:
0.651
Gnomad AMR
AF:
0.727
Gnomad ASJ
AF:
0.552
Gnomad EAS
AF:
0.925
Gnomad SAS
AF:
0.752
Gnomad FIN
AF:
0.711
Gnomad MID
AF:
0.513
Gnomad NFE
AF:
0.629
Gnomad OTH
AF:
0.633
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.639
AC:
97136
AN:
152100
Hom.:
31613
Cov.:
32
AF XY:
0.648
AC XY:
48180
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.563
Gnomad4 AMR
AF:
0.727
Gnomad4 ASJ
AF:
0.552
Gnomad4 EAS
AF:
0.925
Gnomad4 SAS
AF:
0.751
Gnomad4 FIN
AF:
0.711
Gnomad4 NFE
AF:
0.629
Gnomad4 OTH
AF:
0.638
Alfa
AF:
0.608
Hom.:
5488
Bravo
AF:
0.635
Asia WGS
AF:
0.811
AC:
2820
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jun 26, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.016
DANN
Benign
0.37

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.

Other links and lift over

dbSNP: rs10131048; hg19: chr14-68257083; API