chr3-183245503-T-C

Variant summary

Our verdict is Benign. Variant got -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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
MCF2L2NM_015078.4 linkuse as main transcriptc.1863-14486A>G intron_variant ENST00000328913.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MCF2L2ENST00000328913.8 linkuse as main transcriptc.1863-14486A>G intron_variant 5 NM_015078.4 A2Q86YR7-1
MCF2L2ENST00000447025.6 linkuse as main transcriptc.1863-14486A>G intron_variant 1 Q86YR7-2
MCF2L2ENST00000473233.5 linkuse as main transcriptc.1863-14486A>G intron_variant 5 P4Q86YR7-4
MCF2L2ENST00000488149.5 linkuse as main transcriptn.2125-14291A>G intron_variant, non_coding_transcript_variant 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
Gnomad4 AMR
AF:
0.302
Gnomad4 ASJ
AF:
0.354
Gnomad4 EAS
AF:
0.291
Gnomad4 SAS
AF:
0.384
Gnomad4 FIN
AF:
0.356
Gnomad4 NFE
AF:
0.297
Gnomad4 OTH
AF:
0.327
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

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