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GeneBe

rs925451

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000128.4(F11):c.-2+120G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,060 control chromosomes in the GnomAD database, including 9,058 homozygotes. 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: 𝑓 0.34 ( 9058 hom., cov: 33)
Failed GnomAD Quality Control

Consequence

F11
NM_000128.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00400
Variant links:
Genes affected
F11 (HGNC:3529): (coagulation factor XI) This gene encodes coagulation factor XI of the blood coagulation cascade. This protein is present in plasma as a zymogen, which is a unique plasma coagulation enzyme because it exists as a homodimer consisting of two identical polypeptide chains linked by disulfide bonds. During activation of the plasma factor XI, an internal peptide bond is cleaved by factor XIIa (or XII) in each of the two chains, resulting in activated factor XIa, a serine protease composed of two heavy and two light chains held together by disulfide bonds. This activated plasma factor XI triggers the middle phase of the intrisic pathway of blood coagulation by activating factor IX. Defects in this factor lead to Rosenthal syndrome, a blood coagulation abnormality. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
F11NM_000128.4 linkuse as main transcriptc.-2+120G>A intron_variant ENST00000403665.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
F11ENST00000403665.7 linkuse as main transcriptc.-2+120G>A intron_variant 1 NM_000128.4 P1P03951-1
F11ENST00000492972.6 linkuse as main transcriptc.-2+120G>A intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.338
AC:
51289
AN:
151942
Hom.:
9041
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.227
Gnomad AMI
AF:
0.486
Gnomad AMR
AF:
0.358
Gnomad ASJ
AF:
0.361
Gnomad EAS
AF:
0.331
Gnomad SAS
AF:
0.283
Gnomad FIN
AF:
0.413
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.389
Gnomad OTH
AF:
0.363
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.338
AC:
51339
AN:
152060
Hom.:
9058
Cov.:
33
AF XY:
0.337
AC XY:
25050
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.228
Gnomad4 AMR
AF:
0.358
Gnomad4 ASJ
AF:
0.361
Gnomad4 EAS
AF:
0.331
Gnomad4 SAS
AF:
0.283
Gnomad4 FIN
AF:
0.413
Gnomad4 NFE
AF:
0.389
Gnomad4 OTH
AF:
0.367
Alfa
AF:
0.375
Hom.:
14535
Bravo
AF:
0.328
Asia WGS
AF:
0.330
AC:
1149
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
2.0
Dann
Benign
0.65

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs925451; hg19: chr4-187187569; API