Genetic Variant MCF2L:c.*1991T>C (chr13-113098850-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001112732.3(MCF2L):c.*1991T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,016 control chromosomes in the GnomAD database, including 1,823 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 0.15 ( 1821 hom., cov: 34)

Exomes 𝑓: 0.14 ( 2 hom. )

Consequence

MCF2L
NM_001112732.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.92

Variant links:

Genes affected

MCF2L (HGNC:14576): (MCF.2 cell line derived transforming sequence like) This gene encodes a guanine nucleotide exchange factor that interacts specifically with the GTP-bound Rac1 and plays a role in the Rho/Rac signaling pathways. A variant in this gene was associated with osteoarthritis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

MCF2L links:

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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 (SAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCF2L	NM_001112732.3 link	c.*1991T>C		3_prime_UTR_variant	Exon 30 of 30	ENST00000535094.7	NP_001106203.2	O15068-9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCF2L	ENST00000535094.7 link	c.*1991T>C		3_prime_UTR_variant	Exon 30 of 30	2	NM_001112732.3	ENSP00000440374.2		O15068-9

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22154

AN:

151812

Hom.:

1816

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.0380

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.0725

Gnomad MID

AF:

0.258

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.156

GnomAD4 exome

AF:

0.143

AC:

AN:

Hom.:

Cov.:

AF XY:

0.140

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.0714

Gnomad4 NFE exome

AF:

0.227

Gnomad4 OTH exome

AF:

0.222

GnomAD4 genome

AF:

0.146

AC:

22183

AN:

151932

Hom.:

1821

Cov.:

AF XY:

0.145

AC XY:

10781

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.198

Gnomad4 AMR

AF:

0.136

Gnomad4 ASJ

AF:

0.192

Gnomad4 EAS

AF:

0.0381

Gnomad4 SAS

AF:

0.277

Gnomad4 FIN

AF:

0.0725

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.155

Alfa

AF:

0.140

Hom.:

842

Bravo

AF:

0.150

Asia WGS

AF:

0.164

AC:

568

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

0.30

DANN

Benign

0.53

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over