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GeneBe

rs6025

chr1-169549811-C-Achr1-169549811-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2_SupportingPM5BP4_Moderate

The NM_000130.5(F5):c.1601G>T(p.Arg534Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R534Q) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 32)

Consequence

F5
NM_000130.5 missense

Scores

2
1
3

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.48

Links

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.
PM5
?
Other missense variant is known to change same aminoacid residue: Variant chr1-169549811-C-T is described in ClinVar as [drug_response]. Clinvar id is 642. Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=11, risk_factor=1, drug_response=1, Pathogenic_low_penetrance=1}.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.23257288).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
F5NM_000130.5 linkuse as main transcriptc.1601G>T p.Arg534Leu missense_variant 10/25 ENST00000367797.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
F5ENST00000367797.9 linkuse as main transcriptc.1601G>T p.Arg534Leu missense_variant 10/251 NM_000130.5 P2
F5ENST00000367796.3 linkuse as main transcriptc.1601G>T p.Arg534Leu missense_variant 10/255 A2

Frequencies

GnomAD3 genomes
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.64
BayesDel_noAF
Pathogenic
0.15
Cadd
Uncertain
25
DEOGEN2
Benign
0.42
T;T
LIST_S2
Benign
0.83
T;T
MetaRNN
Benign
0.23
T;T
Sift4G
Uncertain
0.0060
D;D
Vest4
0.34
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
gMVP
0.89

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.23
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.23
Position offset: 25

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: rs6025; hg19: chr1-169519049;