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GeneBe

1-11788023-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001010881(C1orf167):c.3824G>A(p.Ser1275Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 152232 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0013 ( 1 hom. )

Consequence

C1orf167
NM_001010881 missense

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.51

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.0053456426).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
C1orf167NM_001010881.2 linkuse as main transcriptc.3824G>A p.Ser1275Asn missense_variant 18/21 ENST00000688073.1
MTHFRNM_005957.5 linkuse as main transcriptc.*2657C>T 3_prime_UTR_variant 12/12 ENST00000376590.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
C1orf167ENST00000688073.1 linkuse as main transcriptc.3824G>A p.Ser1275Asn missense_variant 18/21 NM_001010881.2 A2
MTHFRENST00000376590.9 linkuse as main transcriptc.*2657C>T 3_prime_UTR_variant 12/121 NM_005957.5 A1P42898-1

Frequencies

GnomAD3 genomes
AF:
0.00120
AC:
182
AN:
152232
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000314
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000327
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.000942
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.00207
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.00125
AC:
185
AN:
147914
Hom.:
1
AF XY:
0.00119
AC XY:
95
AN XY:
79538
show subpopulations
Gnomad AFR exome
AF:
0.000447
Gnomad AMR exome
AF:
0.000294
Gnomad ASJ exome
AF:
0.00199
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000996
Gnomad FIN exome
AF:
0.00175
Gnomad NFE exome
AF:
0.00184
Gnomad OTH exome
AF:
0.00118
GnomAD4 exome
AF:
0.00135
AC:
1551
AN:
1148882
Hom.:
3
AF XY:
0.00135
AC XY:
763
AN XY:
563252
show subpopulations
Gnomad4 AFR exome
AF:
0.000206
Gnomad4 AMR exome
AF:
0.000253
Gnomad4 ASJ exome
AF:
0.00179
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00108
Gnomad4 FIN exome
AF:
0.00165
Gnomad4 NFE exome
AF:
0.00143
Gnomad4 OTH exome
AF:
0.00133
Alfa
AF:
0.00155
Hom.:
0
Bravo
AF:
0.00110
TwinsUK
AF:
0.00216
AC:
8
ALSPAC
AF:
0.00104
AC:
4
ExAC
AF:
0.00118
AC:
28
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Homocystinuria due to methylene tetrahydrofolate reductase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingBaylor GeneticsJun 11, 2018This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.61
T
BayesDel_noAF
Benign
-0.65
Cadd
Benign
13
Dann
Benign
0.87
DEOGEN2
Benign
0.0018
T
Eigen
Benign
-0.76
Eigen_PC
Benign
-0.83
FATHMM_MKL
Benign
0.28
N
LIST_S2
Benign
0.36
T
M_CAP
Benign
0.031
D
MetaRNN
Benign
0.0053
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.69
N
MutationTaster
Benign
1.0
N;N;N;N
PROVEAN
Benign
-0.94
N
REVEL
Benign
0.071
Sift
Pathogenic
0.0
D
Sift4G
Benign
0.14
T
Polyphen
0.57
P
Vest4
0.044
MVP
0.067
MPC
0.55
ClinPred
0.027
T
GERP RS
2.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.027
gMVP
0.078

Splicing

Find out SpliceAI 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: rs371188005; hg19: chr1-11848080; COSMIC: COSV57172189; COSMIC: COSV57172189;