rs35069869
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015078.4(MCF2L2):c.1863-14486A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,714 control chromosomes in the GnomAD database, including 8,848 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.34 ( 8848 hom., cov: 31)
Consequence
MCF2L2
NM_015078.4 intron
NM_015078.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.00
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCF2L2 | ENST00000328913.8 | c.1863-14486A>G | intron_variant | Intron 15 of 29 | 5 | NM_015078.4 | ENSP00000328118.3 | |||
MCF2L2 | ENST00000447025.6 | c.1863-14486A>G | intron_variant | Intron 15 of 17 | 1 | ENSP00000388190.2 | ||||
MCF2L2 | ENST00000473233.5 | c.1863-14486A>G | intron_variant | Intron 15 of 28 | 5 | ENSP00000420070.1 | ||||
MCF2L2 | ENST00000488149.5 | n.2125-14291A>G | intron_variant | Intron 16 of 27 | 2 |
Frequencies
GnomAD3 genomes AF: 0.337 AC: 51096AN: 151596Hom.: 8837 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
51096
AN:
151596
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.337 AC: 51149AN: 151714Hom.: 8848 Cov.: 31 AF XY: 0.340 AC XY: 25218AN XY: 74124 show subpopulations
GnomAD4 genome
AF:
AC:
51149
AN:
151714
Hom.:
Cov.:
31
AF XY:
AC XY:
25218
AN XY:
74124
Gnomad4 AFR
AF:
AC:
0.412768
AN:
0.412768
Gnomad4 AMR
AF:
AC:
0.302347
AN:
0.302347
Gnomad4 ASJ
AF:
AC:
0.353602
AN:
0.353602
Gnomad4 EAS
AF:
AC:
0.291392
AN:
0.291392
Gnomad4 SAS
AF:
AC:
0.384407
AN:
0.384407
Gnomad4 FIN
AF:
AC:
0.355592
AN:
0.355592
Gnomad4 NFE
AF:
AC:
0.297107
AN:
0.297107
Gnomad4 OTH
AF:
AC:
0.32654
AN:
0.32654
Heterozygous variant carriers
0
1684
3369
5053
6738
8422
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
506
1012
1518
2024
2530
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1119
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at