11-63764893-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001144936.2(ZFTA):​c.999G>A​(p.Leu333Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000408 in 1,519,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000039 ( 0 hom. )

Consequence

ZFTA
NM_001144936.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.00300
Variant links:
Genes affected
ZFTA (HGNC:28449): (zinc finger translocation associated) Predicted to be involved in negative regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 11-63764893-C-T is Benign according to our data. Variant chr11-63764893-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2641902.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.003 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZFTANM_001144936.2 linkc.999G>A p.Leu333Leu synonymous_variant Exon 3 of 5 ENST00000433688.2 NP_001138408.1 C9JLR9
ZFTAXM_047427478.1 linkc.999G>A p.Leu333Leu synonymous_variant Exon 3 of 4 XP_047283434.1
ZFTAXM_047427477.1 linkc.638-295G>A intron_variant Intron 2 of 3 XP_047283433.1
ZFTAXM_024448662.2 linkc.637+914G>A intron_variant Intron 2 of 2 XP_024304430.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZFTAENST00000433688.2 linkc.999G>A p.Leu333Leu synonymous_variant Exon 3 of 5 5 NM_001144936.2 ENSP00000482180.1 C9JLR9
ZFTAENST00000338498.6 linkc.154+914G>A intron_variant Intron 1 of 1 1 ENSP00000483097.1 A0A087X051
ZFTAENST00000445014.3 linkc.384G>A p.Leu128Leu synonymous_variant Exon 3 of 4 5 ENSP00000478462.1 A0A087WU89

Frequencies

GnomAD3 genomes
AF:
0.0000526
AC:
8
AN:
152166
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000166
AC:
19
AN:
114802
Hom.:
0
AF XY:
0.000176
AC XY:
11
AN XY:
62454
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000185
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00151
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000395
AC:
54
AN:
1367252
Hom.:
0
Cov.:
31
AF XY:
0.0000416
AC XY:
28
AN XY:
672558
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000121
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00119
Gnomad4 SAS exome
AF:
0.0000397
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000375
Gnomad4 OTH exome
AF:
0.0000176
GnomAD4 genome
AF:
0.0000525
AC:
8
AN:
152284
Hom.:
0
Cov.:
33
AF XY:
0.0000403
AC XY:
3
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000653
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000147
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Jan 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

ZFTA: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
3.2
DANN
Benign
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs750754013; hg19: chr11-63532365; API