NM_001242532.5:c.316G>T

Variant names:

• chr17-76742024-G-T
• NM_001242532.5:c.316G>T

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_001242532.5(MFSD11):​c.316G>T​(p.Val106Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MFSD11 NM_001242532.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 9.56
• Publications: 0 publications found

Genes affected

MFSD11 (HGNC:25458): (major facilitator superfamily domain containing 11) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.865

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242532.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD11	NM_001242532.5	MANE Select	c.316G>T	p.Val106Phe	missense	Exon 4 of 13	NP_001229461.1	O43934-1
	MFSD11	NM_001242533.3		c.316G>T	p.Val106Phe	missense	Exon 5 of 14	NP_001229462.1	O43934-1
	MFSD11	NM_001242534.3		c.316G>T	p.Val106Phe	missense	Exon 5 of 14	NP_001229463.1	O43934-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD11	ENST00000685175.1	MANE Select	c.316G>T	p.Val106Phe	missense	Exon 4 of 13	ENSP00000508960.1	O43934-1
	MFSD11	ENST00000336509.8	TSL:1	c.316G>T	p.Val106Phe	missense	Exon 5 of 14	ENSP00000337240.3	O43934-1
	MFSD11	ENST00000590514.5	TSL:1	c.316G>T	p.Val106Phe	missense	Exon 5 of 14	ENSP00000468309.1	O43934-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Benign	0.20	T
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.65
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.97	D
M_CAP	Uncertain	0.12	D
MetaRNN	Pathogenic	0.87	D
MetaSVM	Uncertain	0.11	D
MutationAssessor	Uncertain	2.5	M
PhyloP100		9.6
PrimateAI	Pathogenic	0.82	D
PROVEAN	Uncertain	-3.5	D
REVEL	Pathogenic	0.79
Sift	Uncertain	0.0060	D
Sift4G	Benign	0.10	T
Polyphen		0.078	B
Vest4		0.96
MutPred		0.63		Loss of stability (P = 0.2896)
MVP		0.91
MPC		0.73
ClinPred		0.99	D
GERP RS		5.5
Varity_R		0.64
gMVP		0.96

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

Other links and lift over

hg19: chr17-74738106;