1-16975285-A-T

Variant names:

• chr1-16975285-A-T
• rs761422
• NM_002403.4:c.432T>A

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_002403.4(MFAP2):​c.432T>A​(p.His144Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: MFAP2 NM_002403.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 40 publications found

Genes affected

MFAP2 (HGNC:7033): (microfibril associated protein 2) Microfibrillar-associated protein 2 is a major antigen of elastin-associated microfibrils and a candidate for involvement in the etiology of inherited connective tissue diseases. Four transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.33598992).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MFAP2	NM_002403.4	c.432T>A	p.His144Gln	missense_variant	Exon 8 of 9	ENST00000375535.4	NP_002394.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFAP2	ENST00000375535.4	c.432T>A	p.His144Gln	missense_variant	Exon 8 of 9	1	NM_002403.4	ENSP00000364685.3
MFAP2	ENST00000375534.7	c.429T>A	p.His143Gln	missense_variant	Exon 7 of 8	2		ENSP00000364684.3
MFAP2	ENST00000490075.5	n.1833T>A		non_coding_transcript_exon_variant	Exon 5 of 6	2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 50

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 46709

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.39
BayesDel_addAF	Uncertain	0.094	D
BayesDel_noAF	Benign	-0.10
CADD	Benign	3.2
DANN	Benign	0.87
DEOGEN2	Benign	0.41	.;T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.20	N
LIST_S2	Benign	0.72	T;T
M_CAP	Benign	0.027	D
MetaRNN	Benign	0.34	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.4	.;M
PhyloP100		-0.37
PrimateAI	Uncertain	0.74	T
PROVEAN	Benign	-0.090	N;N
REVEL	Uncertain	0.33
Sift	Benign	0.078	T;T
Sift4G	Benign	0.11	T;T
Polyphen		0.0010	.;B
Vest4		0.50
MutPred		0.41		.;Gain of relative solvent accessibility (P = 0.2363);
MVP		0.081
MPC		0.32
ClinPred		0.48	T
GERP RS		-4.4
Varity_R		0.19
gMVP		0.36
Mutation Taster		=55/45	polymorphism

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

Other links and lift over

dbSNP: rs761422; hg19: chr1-17301780;