X-54116727-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_017848.6(FAM120C):​c.2130G>A​(p.Val710Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,209,764 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0000090 ( 0 hom., 1 hem., cov: 22)
Exomes 𝑓: 0.000014 ( 0 hom. 5 hem. )

Consequence

FAM120C
NM_017848.6 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.146
Variant links:
Genes affected
FAM120C (HGNC:16949): (family with sequence similarity 120 member C) This gene encodes a potential transmembrane protein and lies in a region where mutations and deletions have been associated with intellectual disability and autism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
Variant X-54116727-C-T is Benign according to our data. Variant chrX-54116727-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2660653.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.146 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 5 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM120CNM_017848.6 linkc.2130G>A p.Val710Val synonymous_variant Exon 10 of 16 ENST00000375180.7 NP_060318.4 Q9NX05-1
FAM120CNM_001300788.2 linkc.2130G>A p.Val710Val synonymous_variant Exon 10 of 14 NP_001287717.1 F8W881
FAM120CXM_006724589.5 linkc.2130G>A p.Val710Val synonymous_variant Exon 10 of 15 XP_006724652.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM120CENST00000375180.7 linkc.2130G>A p.Val710Val synonymous_variant Exon 10 of 16 1 NM_017848.6 ENSP00000364324.2 Q9NX05-1
FAM120CENST00000328235.4 linkc.2130G>A p.Val710Val synonymous_variant Exon 10 of 14 1 ENSP00000329896.4 F8W881

Frequencies

GnomAD3 genomes
AF:
0.00000896
AC:
1
AN:
111608
Hom.:
0
Cov.:
22
AF XY:
0.0000296
AC XY:
1
AN XY:
33794
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:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000188
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000137
AC:
15
AN:
1098156
Hom.:
0
Cov.:
30
AF XY:
0.0000138
AC XY:
5
AN XY:
363512
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000166
Gnomad4 OTH exome
AF:
0.0000217
GnomAD4 genome
AF:
0.00000896
AC:
1
AN:
111608
Hom.:
0
Cov.:
22
AF XY:
0.0000296
AC XY:
1
AN XY:
33794
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000188
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Sep 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

FAM120C: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
4.4
DANN
Benign
0.73

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: rs2066969855; hg19: chrX-54143160; API