2-24017528-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001346880.2(MFSD2B):​c.621C>G​(p.His207Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000049 in 1,427,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 0.0000049 ( 0 hom. )

Consequence

MFSD2B
NM_001346880.2 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0240
Variant links:
Genes affected
MFSD2B (HGNC:37207): (MFSD2 lysolipid transporter B, sphingolipid) Enables sphingolipid transporter activity. Involved in lipid transport. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1504974).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MFSD2BNM_001346880.2 linkc.621C>G p.His207Gln missense_variant Exon 6 of 14 ENST00000338315.6 NP_001333809.1 A6NFX1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MFSD2BENST00000338315.6 linkc.621C>G p.His207Gln missense_variant Exon 6 of 14 5 NM_001346880.2 ENSP00000342501.4 A6NFX1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.0000261
AC:
5
AN:
191396
Hom.:
0
AF XY:
0.0000291
AC XY:
3
AN XY:
103266
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000141
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:
0.0000123
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000490
AC:
7
AN:
1427192
Hom.:
0
Cov.:
32
AF XY:
0.00000566
AC XY:
4
AN XY:
706726
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000101
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:
0.00000274
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.0000508
Hom.:
0
ExAC
AF:
0.0000167
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.37
CADD
Benign
2.9
DANN
Benign
0.83
DEOGEN2
Uncertain
0.47
.;T
Eigen
Benign
-0.92
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.30
N
LIST_S2
Benign
0.68
T;T
M_CAP
Uncertain
0.12
D
MetaRNN
Benign
0.15
T;T
MetaSVM
Benign
-0.56
T
MutationAssessor
Benign
1.5
.;L
PrimateAI
Benign
0.44
T
PROVEAN
Uncertain
-4.0
D;D
REVEL
Benign
0.20
Sift
Uncertain
0.025
D;D
Sift4G
Benign
0.070
T;T
Polyphen
0.037
.;B
Vest4
0.51
MutPred
0.46
Gain of relative solvent accessibility (P = 0.1259);Gain of relative solvent accessibility (P = 0.1259);
MVP
0.26
MPC
0.30
ClinPred
0.051
T
GERP RS
1.4
Varity_R
0.18
gMVP
0.43

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: rs769192324; hg19: chr2-24240398; API