rs35069869

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.00
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 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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MCF2L2NM_015078.4 linkc.1863-14486A>G intron_variant Intron 15 of 29 ENST00000328913.8 NP_055893.4 Q86YR7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MCF2L2ENST00000328913.8 linkc.1863-14486A>G intron_variant Intron 15 of 29 5 NM_015078.4 ENSP00000328118.3 Q86YR7-1
MCF2L2ENST00000447025.6 linkc.1863-14486A>G intron_variant Intron 15 of 17 1 ENSP00000388190.2 Q86YR7-2
MCF2L2ENST00000473233.5 linkc.1863-14486A>G intron_variant Intron 15 of 28 5 ENSP00000420070.1 Q86YR7-4
MCF2L2ENST00000488149.5 linkn.2125-14291A>G intron_variant Intron 16 of 27 2

Frequencies

GnomAD3 genomes
AF:
0.337
AC:
51096
AN:
151596
Hom.:
8837
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.412
Gnomad AMI
AF:
0.248
Gnomad AMR
AF:
0.302
Gnomad ASJ
AF:
0.354
Gnomad EAS
AF:
0.291
Gnomad SAS
AF:
0.386
Gnomad FIN
AF:
0.356
Gnomad MID
AF:
0.294
Gnomad NFE
AF:
0.297
Gnomad OTH
AF:
0.325
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.337
AC:
51149
AN:
151714
Hom.:
8848
Cov.:
31
AF XY:
0.340
AC XY:
25218
AN XY:
74124
show subpopulations
Gnomad4 AFR
AF:
0.413
AC:
0.412768
AN:
0.412768
Gnomad4 AMR
AF:
0.302
AC:
0.302347
AN:
0.302347
Gnomad4 ASJ
AF:
0.354
AC:
0.353602
AN:
0.353602
Gnomad4 EAS
AF:
0.291
AC:
0.291392
AN:
0.291392
Gnomad4 SAS
AF:
0.384
AC:
0.384407
AN:
0.384407
Gnomad4 FIN
AF:
0.356
AC:
0.355592
AN:
0.355592
Gnomad4 NFE
AF:
0.297
AC:
0.297107
AN:
0.297107
Gnomad4 OTH
AF:
0.327
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:
0.316
Hom.:
947
Bravo
AF:
0.334
Asia WGS
AF:
0.322
AC:
1119
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.48
DANN
Benign
0.51
Mutation Taster
=100/0
polymorphism (auto)

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: rs35069869; hg19: chr3-182963291; API