Variant chr12-53253490-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000329548.5(MFSD5):c.655C>G(p.Leu219Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,804 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000082 ( 0 hom. )

Consequence

MFSD5
ENST00000329548.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.05

Variant links:

Genes affected

MFSD5 (HGNC:28156): (major facilitator superfamily domain containing 5) Predicted to enable molybdate ion transmembrane transporter activity. Predicted to be involved in molybdate ion transport. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

MFSD5 links:

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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=0.13938144).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MFSD5	NM_032889.5 linkuse as main transcript	c.655C>G	p.Leu219Val	missense_variant	2/2	ENST00000329548.5	NP_116278.3	Q6N075-1
MFSD5	NM_001170790.2 linkuse as main transcript	c.976C>G	p.Leu326Val	missense_variant	2/2		NP_001164261.1	Q6N075-2
MFSD5	XM_005269197.2 linkuse as main transcript	c.976C>G	p.Leu326Val	missense_variant	3/3		XP_005269254.1	Q6N075-2
MFSD5	XM_005269198.5 linkuse as main transcript	c.655C>G	p.Leu219Val	missense_variant	2/2		XP_005269255.1	Q6N075-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MFSD5	ENST00000329548.5 linkuse as main transcript	c.655C>G	p.Leu219Val	missense_variant	2/2	1	NM_032889.5	ENSP00000332624.5	Q6N075-1
MFSD5	ENST00000534842.1 linkuse as main transcript	c.976C>G	p.Leu326Val	missense_variant	2/2	2		ENSP00000442688.1	Q6N075-2
MFSD5	ENST00000551660.2 linkuse as main transcript	c.976C>G	p.Leu326Val	missense_variant	2/2	2		ENSP00000449354.2	F8VV69

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000597

AC:

AN:

251100

Hom.:

AF XY:

0.0000516

AC XY:

AN XY:

135764

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000816

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000821

AC:

AN:

1461804

Hom.:

Cov.:

AF XY:

0.00000825

AC XY:

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000302

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.0000151

ExAC

AF:

0.0000494

AC:

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

Sep 12, 2023

The c.976C>G (p.L326V) alteration is located in exon 2 (coding exon 2) of the MFSD5 gene. This alteration results from a C to G substitution at nucleotide position 976, causing the leucine (L) at amino acid position 326 to be replaced by a valine (V). 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

0.088

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.73

DEOGEN2

Benign

0.018

.;T;T

Eigen

Benign

-0.14

Eigen_PC

Benign

-0.017

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.66

T;T;T

M_CAP

Benign

0.022

MetaRNN

Benign

0.14

T;T;T

MetaSVM

Benign

-0.49

MutationAssessor

Benign

1.7

.;.;L

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-0.43

N;N;N

REVEL

Benign

0.24

Sift

Benign

0.090

T;T;T

Sift4G

Benign

0.51

T;T;T

Polyphen

0.014

.;.;B

Vest4

0.10

MutPred

0.74

.;.;Loss of stability (P = 0.0972);

MVP

0.53

MPC

0.27

ClinPred

0.041

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.12

gMVP

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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