Variant 2-240887078-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001085437.3(MAB21L4):c.1336G>A(p.Glu446Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,613,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00011 ( 0 hom. )

Consequence

MAB21L4
NM_001085437.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.201

Variant links:

Genes affected

MAB21L4 (HGNC:26216): (mab-21 like 4)

MAB21L4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.0402402).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MAB21L4	NM_001085437.3 linkuse as main transcript	c.1336G>A	p.Glu446Lys	missense_variant	5/5	ENST00000388934.5	NP_001078906.3
MAB21L4	NM_001282921.2 linkuse as main transcript	c.889G>A	p.Glu297Lys	missense_variant	5/5		NP_001269850.2
MAB21L4	NM_024861.4 linkuse as main transcript	c.832G>A	p.Glu278Lys	missense_variant	5/5		NP_079137.4
MAB21L4	XM_011511877.2 linkuse as main transcript	c.1336G>A	p.Glu446Lys	missense_variant	6/6		XP_011510179.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAB21L4	ENST00000388934.5 linkuse as main transcript	c.1336G>A	p.Glu446Lys	missense_variant	5/5	2	NM_001085437.3	ENSP00000373586	P1	Q08AI8-1
MAB21L4	ENST00000307486.12 linkuse as main transcript	c.889G>A	p.Glu297Lys	missense_variant	5/5	1		ENSP00000302779		Q08AI8-2
MAB21L4	ENST00000402775.6 linkuse as main transcript	c.832G>A	p.Glu278Lys	missense_variant	5/5	2		ENSP00000385338		Q08AI8-3

Frequencies

GnomAD3 genomes

AF:

0.0000394

AC:

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

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:

0.0000882

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000523

AC:

AN:

248664

Hom.:

AF XY:

0.0000445

AC XY:

AN XY:

134982

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000290

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:

0.0000978

Gnomad OTH exome

AF:

0.000165

GnomAD4 exome

AF:

0.000112

AC:

163

AN:

1461656

Hom.:

Cov.:

AF XY:

0.0000908

AC XY:

AN XY:

727164

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000224

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:

0.000141

Gnomad4 OTH exome

AF:

0.0000828

GnomAD4 genome

AF:

0.0000394

AC:

AN:

152342

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.00

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:

0.0000882

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000141

Hom.:

Bravo

AF:

0.0000264

ExAC

AF:

0.0000414

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.000296

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 submitter

clinical testing

Ambry Genetics

Oct 06, 2021

The c.1336G>A (p.E446K) alteration is located in exon 5 (coding exon 5) of the C2orf54 gene. This alteration results from a G to A substitution at nucleotide position 1336, causing the glutamic acid (E) at amino acid position 446 to be replaced by a lysine (K). 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

0.091

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.50

CADD

Benign

7.3

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0029

.;.;T

Eigen

Benign

-0.83

Eigen_PC

Benign

-0.81

FATHMM_MKL

Benign

0.036

LIST_S2

Benign

0.47

T;T;T

M_CAP

Benign

0.0091

MetaRNN

Benign

0.040

T;T;T

MetaSVM

Benign

-0.99

MutationTaster

Benign

1.0

N;N;N

PROVEAN

Benign

-0.75

N;N;N

REVEL

Benign

0.049

Sift

Benign

0.11

T;T;T

Sift4G

Benign

0.073

T;T;T

Polyphen

0.034

B;.;B

Vest4

0.065

MVP

0.14

MPC

0.079

ClinPred

0.063

GERP RS

2.6

Varity_R

0.083

gMVP

0.29

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over