NM_001100607.3:c.641G>T

Variant names:

• chr14-94289953-C-A
• NM_001100607.3:c.641G>T

Variant summary

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

The NM_001100607.3(SERPINA10):​c.641G>T​(p.Arg214Leu) 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: 33)
• Consequence: SERPINA10 NM_001100607.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

Genes affected

SERPINA10 (HGNC:15996): (serpin family A member 10) The protein encoded by this gene belongs to the serpin family. It is predominantly expressed in the liver and secreted in plasma. It inhibits the activity of coagulation factors Xa and XIa in the presence of protein Z, calcium and phospholipid. Mutations in this gene are associated with venous thrombosis. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, May 2010]

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=0.24977791).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINA10	NM_001100607.3	c.641G>T	p.Arg214Leu	missense_variant	Exon 2 of 5	ENST00000261994.9	NP_001094077.1
SERPINA10	NM_016186.3	c.641G>T	p.Arg214Leu	missense_variant	Exon 2 of 5		NP_057270.1
SERPINA10	XM_017021353.2	c.761G>T	p.Arg254Leu	missense_variant	Exon 3 of 6		XP_016876842.1
SERPINA10	XM_005267733.6	c.641G>T	p.Arg214Leu	missense_variant	Exon 2 of 5		XP_005267790.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINA10	ENST00000261994.9	c.641G>T	p.Arg214Leu	missense_variant	Exon 2 of 5	1	NM_001100607.3	ENSP00000261994.4
SERPINA10	ENST00000554723.5	c.761G>T	p.Arg254Leu	missense_variant	Exon 2 of 5	1		ENSP00000450896.1
SERPINA10	ENST00000393096.5	c.641G>T	p.Arg214Leu	missense_variant	Exon 2 of 5	1		ENSP00000376809.1
SERPINA10	ENST00000554173.1	c.641G>T	p.Arg214Leu	missense_variant	Exon 1 of 4	1		ENSP00000450971.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	0.014
DANN	Benign	0.96
DEOGEN2	Benign	0.36	T;.;T;T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.056	N
LIST_S2	Benign	0.43	.;T;T;.
M_CAP	Benign	0.047	D
MetaRNN	Benign	0.25	T;T;T;T
MetaSVM	Benign	-0.68	T
MutationAssessor	Benign	1.1	L;.;L;L
PrimateAI	Benign	0.20	T
PROVEAN	Uncertain	-3.3	D;D;D;D
REVEL	Benign	0.15
Sift	Benign	0.090	T;D;T;T
Sift4G	Benign	0.14	T;T;T;T
Polyphen		0.065	B;.;B;B
Vest4		0.17
MutPred		0.50		Loss of MoRF binding (P = 0.0224);.;Loss of MoRF binding (P = 0.0224);Loss of MoRF binding (P = 0.0224);
MVP		0.18
MPC		0.031
ClinPred		0.057	T
GERP RS		-3.9
Varity_R		0.19
gMVP		0.33

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-94756290;