rs782270709

Variant names:

• chrX-154837617-C-G
• rs782270709
• NM_000132.4:c.7036G>C

Your query was ambiguous. Multiple possible variants found:

• chrX-154837617-C-G
• chrX-154837617-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1 PM2 BP4_Moderate

The NM_000132.4(F8):​c.7036G>C​(p.Glu2346Gln) 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. 13/20 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: 22)
• Consequence: F8 NM_000132.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.36

Genes affected

F8 (HGNC:3546): (coagulation factor VIII) This gene encodes coagulation factor VIII, which participates in the intrinsic pathway of blood coagulation; factor VIII is a cofactor for factor IXa which, in the presence of Ca+2 and phospholipids, converts factor X to the activated form Xa. This gene produces two alternatively spliced transcripts. Transcript variant 1 encodes a large glycoprotein, isoform a, which circulates in plasma and associates with von Willebrand factor in a noncovalent complex. This protein undergoes multiple cleavage events. Transcript variant 2 encodes a putative small protein, isoform b, which consists primarily of the phospholipid binding domain of factor VIIIc. This binding domain is essential for coagulant activity. Defects in this gene results in hemophilia A, a common recessive X-linked coagulation disorder. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a strand (size 8) in uniprot entity FA8_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in NM_000132.4
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2611032).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F8	NM_000132.4	c.7036G>C	p.Glu2346Gln	missense_variant	Exon 26 of 26	ENST00000360256.9	NP_000123.1
F8	NM_019863.3	c.631G>C	p.Glu211Gln	missense_variant	Exon 5 of 5		NP_063916.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
F8	ENST00000360256.9	c.7036G>C	p.Glu2346Gln	missense_variant	Exon 26 of 26	1	NM_000132.4	ENSP00000353393.4
F8	ENST00000330287.10	c.631G>C	p.Glu211Gln	missense_variant	Exon 5 of 5	1		ENSP00000327895.6
F8	ENST00000644698.1	c.769G>C	p.Glu257Gln	missense_variant	Exon 6 of 6			ENSP00000495706.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Uncertain	0.050	T
BayesDel_noAF	Benign	-0.17
CADD	Benign	11
DANN	Benign	0.97
DEOGEN2	Uncertain	0.49	.;T;.
FATHMM_MKL	Benign	0.092	N
LIST_S2	Benign	0.71	T;T;T
M_CAP	Uncertain	0.20	D
MetaRNN	Benign	0.26	T;T;T
MetaSVM	Uncertain	0.28	D
MutationAssessor	Benign	1.2	.;L;.
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-1.9	N;N;.
REVEL	Benign	0.25
Sift	Uncertain	0.024	D;T;.
Sift4G	Benign	0.11	T;D;.
Polyphen		0.23	.;B;.
Vest4		0.13
MutPred		0.38		.;Loss of sheet (P = 0.0357);.;
MVP		0.87
MPC		0.83
ClinPred		0.24	T
GERP RS		3.9
Varity_R		0.45
gMVP		0.94

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: rs782270709; hg19: chrX-154065892;