chr14-94614699-C-A

Variant names:

• chr14-94614699-C-A
• rs61737405
• NM_001085.5:c.258C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001085.5(SERPINA3):​c.258C>A​(p.Phe86Leu) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SERPINA3 NM_001085.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

Genes affected

SERPINA3 (HGNC:16): (serpin family A member 3) The protein encoded by this gene is a member of the serpin family of proteins, a group of proteins that inhibit serine proteases. This gene is one in a cluster of serpin genes located on the q arm of chromosome 14. Polymorphisms in this protein appear to be tissue specific and influence protease targeting. Variations in this protein's sequence have been implicated in Alzheimer's disease, and deficiency of this protein has been associated with liver disease. Mutations have been identified in patients with Parkinson disease and chronic obstructive pulmonary disease. [provided by RefSeq, Jun 2020]

ENSG00000273259 (HGNC:):

ACMG classification

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=0.22494361).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINA3	NM_001085.5	c.258C>A	p.Phe86Leu	missense_variant	Exon 2 of 5	ENST00000393078.5	NP_001076.2
SERPINA3	NM_001384672.1	c.258C>A	p.Phe86Leu	missense_variant	Exon 2 of 5		NP_001371601.1
SERPINA3	NM_001384673.1	c.258C>A	p.Phe86Leu	missense_variant	Exon 3 of 6		NP_001371602.1
SERPINA3	NM_001384674.1	c.258C>A	p.Phe86Leu	missense_variant	Exon 3 of 6		NP_001371603.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINA3	ENST00000393078.5	c.258C>A	p.Phe86Leu	missense_variant	Exon 2 of 5	1	NM_001085.5	ENSP00000376793.3
ENSG00000273259	ENST00000553947.1	n.*1084C>A		non_coding_transcript_exon_variant	Exon 5 of 8	2		ENSP00000452367.2
ENSG00000273259	ENST00000553947.1	n.*1084C>A		3_prime_UTR_variant	Exon 5 of 8	2		ENSP00000452367.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251352 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135828

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

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: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.60
BayesDel_addAF	Benign	-0.016	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	12
DANN	Benign	0.77
DEOGEN2	Benign	0.19	T;T;.;T
Eigen	Benign	-0.67
Eigen_PC	Benign	-0.49
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Benign	0.60	T;.;T;.
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.22	T;T;T;T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	0.20	N;N;.;N
PrimateAI	Benign	0.34	T
PROVEAN	Benign	-1.6	N;N;N;N
REVEL	Benign	0.20
Sift	Benign	0.91	T;T;T;T
Sift4G	Benign	1.0	T;T;T;T
Polyphen		0.0070	B;B;.;B
Vest4		0.045
MutPred		0.53		Gain of catalytic residue at S81 (P = 6e-04);Gain of catalytic residue at S81 (P = 6e-04);Gain of catalytic residue at S81 (P = 6e-04);Gain of catalytic residue at S81 (P = 6e-04);
MVP		0.69
MPC		0.011
ClinPred		0.10	T
GERP RS		1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.45
gMVP		0.13

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

Other links and lift over

dbSNP: rs61737405; hg19: chr14-95081036;