14-68789706-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_004926.4(ZFP36L1):ā€‹c.844A>Cā€‹(p.Met282Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,116 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 Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.0000066 ( 0 hom., cov: 32)

Consequence

ZFP36L1
NM_004926.4 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.72
Variant links:
Genes affected
ZFP36L1 (HGNC:1107): (ZFP36 ring finger protein like 1) This gene is a member of the TIS11 family of early response genes, which are induced by various agonists such as the phorbol ester TPA and the polypeptide mitogen EGF. This gene is well conserved across species and has a promoter that contains motifs seen in other early-response genes. The encoded protein contains a distinguishing putative zinc finger domain with a repeating cys-his motif. This putative nuclear transcription factor most likely functions in regulating the response to growth factors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.055403292).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZFP36L1NM_004926.4 linkc.844A>C p.Met282Leu missense_variant Exon 2 of 2 ENST00000439696.3 NP_004917.2 Q07352A0A024R658B3KNA8
ZFP36L1NM_001244701.1 linkc.1051A>C p.Met351Leu missense_variant Exon 3 of 3 NP_001231630.1 Q07352
ZFP36L1NM_001244698.2 linkc.844A>C p.Met282Leu missense_variant Exon 2 of 3 NP_001231627.1 Q07352A0A024R658B3KNA8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZFP36L1ENST00000439696.3 linkc.844A>C p.Met282Leu missense_variant Exon 2 of 2 1 NM_004926.4 ENSP00000388402.2 Q07352
ZFP36L1ENST00000336440.4 linkc.844A>C p.Met282Leu missense_variant Exon 2 of 3 2 ENSP00000337386.3 Q07352
ZFP36L1ENST00000555997.1 linkn.1048A>C non_coding_transcript_exon_variant Exon 2 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
151996
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000242
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000399
AC:
1
AN:
250318
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135712
show subpopulations
Gnomad AFR exome
AF:
0.0000634
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
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
Cov.:
32
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152116
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.0000241
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:
0.00
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.00000824
AC:
1

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Sep 03, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.844A>C (p.M282L) alteration is located in exon 2 (coding exon 2) of the ZFP36L1 gene. This alteration results from a A to C substitution at nucleotide position 844, causing the methionine (M) at amino acid position 282 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.082
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.39
CADD
Benign
17
DANN
Benign
0.88
DEOGEN2
Benign
0.057
T;T
Eigen
Benign
-0.44
Eigen_PC
Benign
-0.26
FATHMM_MKL
Benign
0.68
D
LIST_S2
Benign
0.85
.;D
M_CAP
Benign
0.011
T
MetaRNN
Benign
0.055
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.52
N;N
PrimateAI
Uncertain
0.70
T
PROVEAN
Benign
0.070
N;N
REVEL
Benign
0.17
Sift
Benign
0.48
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.013
B;B
Vest4
0.23
MutPred
0.31
Gain of catalytic residue at E284 (P = 0.0078);Gain of catalytic residue at E284 (P = 0.0078);
MVP
0.32
MPC
1.1
ClinPred
0.018
T
GERP RS
3.5
Varity_R
0.17
gMVP
0.26

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.

Other links and lift over

dbSNP: rs529187831; hg19: chr14-69256423; API