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GeneBe

1-11788224-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7

The NM_001010881(C1orf167):c.3924C>T(p.His1308=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000236 in 152234 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00015 ( 0 hom. )

Consequence

C1orf167
NM_001010881 synonymous

Scores

2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.115

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP7
?
Synonymous conserved (PhyloP=0.115 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
C1orf167NM_001010881.2 linkuse as main transcriptc.3924C>T p.His1308= synonymous_variant 19/21 ENST00000688073.1
MTHFRNM_005957.5 linkuse as main transcriptc.*2456G>A 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.3924C>T p.His1308= synonymous_variant 19/21 NM_001010881.2 A2
MTHFRENST00000376590.9 linkuse as main transcriptc.*2456G>A 3_prime_UTR_variant 12/121 NM_005957.5 A1P42898-1

Frequencies

GnomAD3 genomes
AF:
0.000236
AC:
36
AN:
152234
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000514
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000148
AC:
22
AN:
148972
Hom.:
0
AF XY:
0.000162
AC XY:
13
AN XY:
80200
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000647
Gnomad NFE exome
AF:
0.000356
Gnomad OTH exome
AF:
0.000233
GnomAD4 exome
AF:
0.000200
AC:
230
AN:
1151450
Hom.:
0
AF XY:
0.000218
AC XY:
123
AN XY:
564492
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000628
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000131
Gnomad4 FIN exome
AF:
0.0000731
Gnomad4 NFE exome
AF:
0.000239
Gnomad4 OTH exome
AF:
0.000120
Alfa
AF:
0.000383
Hom.:
0
Bravo
AF:
0.000212

ClinVar

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

Submissions by phenotype

Neural tube defects, folate-sensitive Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
Cadd
Benign
1.4
Dann
Benign
0.63

Splicing

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: rs770536637; hg19: chr1-11848281;