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GeneBe

5-61332312-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_ModerateBP6_Moderate

The NM_020928.2(ZSWIM6):c.40C>T(p.Leu14Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000006 in 1,167,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000049 ( 0 hom. )

Consequence

ZSWIM6
NM_020928.2 missense

Scores

2
17

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.92
Variant links:
Genes affected
ZSWIM6 (HGNC:29316): (zinc finger SWIM-type containing 6) The protein encoded by this gene contains a zinc finger SWI2/SNF2 and MuDR (SWIM) domain. Proteins with SWIM domains have been found in a diverse number of species and are predicted to interact with DNA or proteins. Mutations in this gene result in acromelic frontonasal dysostosis. [provided by RefSeq, Apr 2017]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PP2
Missense variant where missense usually causes diseases, ZSWIM6
BP4
Computational evidence support a benign effect (MetaRNN=0.18052235).
BP6
Variant 5-61332312-C-T is Benign according to our data. Variant chr5-61332312-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1567210.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZSWIM6NM_020928.2 linkuse as main transcriptc.40C>T p.Leu14Phe missense_variant 1/14 ENST00000252744.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZSWIM6ENST00000252744.6 linkuse as main transcriptc.40C>T p.Leu14Phe missense_variant 1/145 NM_020928.2 P1

Frequencies

GnomAD3 genomes
AF:
0.0000133
AC:
2
AN:
150274
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000243
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000148
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000492
AC:
5
AN:
1016942
Hom.:
0
Cov.:
28
AF XY:
0.00
AC XY:
0
AN XY:
481652
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000455
Gnomad4 OTH exome
AF:
0.0000257
GnomAD4 genome
AF:
0.0000133
AC:
2
AN:
150274
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
73354
show subpopulations
Gnomad4 AFR
AF:
0.0000243
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000148
Gnomad4 OTH
AF:
0.00

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeDec 06, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
Cadd
Benign
23
Dann
Benign
0.97
DEOGEN2
Benign
0.0038
T
Eigen
Benign
-0.48
Eigen_PC
Benign
-0.48
FATHMM_MKL
Benign
0.011
N
LIST_S2
Benign
0.73
T
M_CAP
Pathogenic
0.57
D
MetaRNN
Benign
0.18
T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
0.0
N
MutationTaster
Benign
0.77
N
PrimateAI
Pathogenic
0.93
D
PROVEAN
Benign
-0.57
N
REVEL
Benign
0.071
Sift
Benign
0.067
T
Sift4G
Benign
0.39
T
Polyphen
0.51
P
Vest4
0.14
MutPred
0.42
Gain of sheet (P = 0.0827);
MVP
0.10
MPC
0.54
ClinPred
0.28
T
GERP RS
0.38
Varity_R
0.082
gMVP
0.42

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: rs1345013612; hg19: chr5-60628139; API