chr3-183206183-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_015078.4(MCF2L2):ā€‹c.2744G>Cā€‹(p.Arg915Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,614,038 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 Uncertain significance (ā˜…). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R915M) has been classified as Uncertain significance.

Frequency

Genomes: š‘“ 0.000046 ( 0 hom., cov: 32)
Exomes š‘“: 0.000066 ( 0 hom. )

Consequence

MCF2L2
NM_015078.4 missense

Scores

6
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.43
Variant links:
Genes affected
MCF2L2 (HGNC:30319): (MCF.2 cell line derived transforming sequence-like 2) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of catalytic activity. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3007474).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MCF2L2NM_015078.4 linkuse as main transcriptc.2744G>C p.Arg915Thr missense_variant 24/30 ENST00000328913.8
MCF2L2XM_017005943.3 linkuse as main transcriptc.2744G>C p.Arg915Thr missense_variant 24/26
MCF2L2XM_011512585.3 linkuse as main transcriptc.1685G>C p.Arg562Thr missense_variant 16/22
MCF2L2XM_047447751.1 linkuse as main transcriptc.1643G>C p.Arg548Thr missense_variant 15/21

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MCF2L2ENST00000328913.8 linkuse as main transcriptc.2744G>C p.Arg915Thr missense_variant 24/305 NM_015078.4 A2Q86YR7-1
MCF2L2ENST00000473233.5 linkuse as main transcriptc.2744G>C p.Arg915Thr missense_variant 24/295 P4Q86YR7-4
MCF2L2ENST00000468976.5 linkuse as main transcriptn.125G>C non_coding_transcript_exon_variant 2/64
MCF2L2ENST00000488149.5 linkuse as main transcriptn.7191G>C non_coding_transcript_exon_variant 25/282

Frequencies

GnomAD3 genomes
AF:
0.0000460
AC:
7
AN:
152188
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000483
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:
0.0000735
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000318
AC:
8
AN:
251370
Hom.:
0
AF XY:
0.0000221
AC XY:
3
AN XY:
135854
show subpopulations
Gnomad AFR exome
AF:
0.00
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:
0.0000704
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000657
AC:
96
AN:
1461850
Hom.:
0
Cov.:
31
AF XY:
0.0000619
AC XY:
45
AN XY:
727230
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:
0.0000827
Gnomad4 OTH exome
AF:
0.0000662
GnomAD4 genome
AF:
0.0000460
AC:
7
AN:
152188
Hom.:
0
Cov.:
32
AF XY:
0.0000269
AC XY:
2
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.0000483
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:
0.0000735
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000227
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0
ExAC
AF:
0.0000412
AC:
5
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJan 24, 2023The c.2744G>C (p.R915T) alteration is located in exon 24 (coding exon 24) of the MCF2L2 gene. This alteration results from a G to C substitution at nucleotide position 2744, causing the arginine (R) at amino acid position 915 to be replaced by a threonine (T). 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
0.27
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.42
CADD
Uncertain
23
DANN
Uncertain
0.98
DEOGEN2
Benign
0.063
T;.
Eigen
Uncertain
0.21
Eigen_PC
Benign
0.16
FATHMM_MKL
Benign
0.58
D
LIST_S2
Benign
0.78
T;T
M_CAP
Benign
0.0073
T
MetaRNN
Benign
0.30
T;T
MetaSVM
Benign
-0.91
T
MutationAssessor
Uncertain
2.4
M;M
MutationTaster
Benign
0.72
N;N
PrimateAI
Benign
0.34
T
PROVEAN
Uncertain
-2.9
D;D
REVEL
Benign
0.12
Sift
Uncertain
0.0010
D;D
Sift4G
Uncertain
0.0030
D;D
Polyphen
0.95
P;.
Vest4
0.46
MutPred
0.44
Loss of MoRF binding (P = 0.0262);Loss of MoRF binding (P = 0.0262);
MVP
0.40
MPC
0.57
ClinPred
0.79
D
GERP RS
2.5
Varity_R
0.26
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.10
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: rs746462556; hg19: chr3-182923971; API