12-8222185-C-CACG

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1

The NM_018088.3(FAM90A1):​c.1031_1032insCGT​(p.Thr344_Ser345insVal) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.53 ( 23703 hom., cov: 0)
Exomes 𝑓: 0.68 ( 326290 hom. )
Failed GnomAD Quality Control

Consequence

FAM90A1
NM_018088.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.63
Variant links:
Genes affected
FAM90A1 (HGNC:25526): (family with sequence similarity 90 member A1) FAM90A1 belongs to subfamily I of the primate-specific FAM90A gene family, which originated from multiple duplications and rearrangements (Bosch et al., 2007 [PubMed 17684299]).[supplied by OMIM, Oct 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM4
Nonframeshift variant in NON repetitive region in NM_018088.3. Strenght limited to Supporting due to length of the change: 1aa.
BP6
Variant 12-8222185-C-CACG is Benign according to our data. Variant chr12-8222185-C-CACG is described in ClinVar as [Benign]. Clinvar id is 768513.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM90A1NM_018088.3 linkc.1031_1032insCGT p.Thr344_Ser345insVal disruptive_inframe_insertion Exon 7 of 7 ENST00000538603.6 NP_060558.3 Q86YD7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM90A1ENST00000538603.6 linkc.1031_1032insCGT p.Thr344_Ser345insVal disruptive_inframe_insertion Exon 7 of 7 1 NM_018088.3 ENSP00000445418.1 Q86YD7
FAM90A1ENST00000307435.10 linkc.1031_1032insCGT p.Thr344_Ser345insVal disruptive_inframe_insertion Exon 6 of 6 2 ENSP00000307798.6 Q86YD7

Frequencies

GnomAD3 genomes
AF:
0.526
AC:
79918
AN:
151812
Hom.:
23709
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.697
Gnomad AMR
AF:
0.501
Gnomad ASJ
AF:
0.618
Gnomad EAS
AF:
0.534
Gnomad SAS
AF:
0.462
Gnomad FIN
AF:
0.656
Gnomad MID
AF:
0.623
Gnomad NFE
AF:
0.723
Gnomad OTH
AF:
0.569
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.677
AC:
987221
AN:
1459264
Hom.:
326290
Cov.:
80
AF XY:
0.672
AC XY:
488091
AN XY:
725930
show subpopulations
Gnomad4 AFR exome
AF:
0.151
Gnomad4 AMR exome
AF:
0.437
Gnomad4 ASJ exome
AF:
0.631
Gnomad4 EAS exome
AF:
0.525
Gnomad4 SAS exome
AF:
0.466
Gnomad4 FIN exome
AF:
0.665
Gnomad4 NFE exome
AF:
0.728
Gnomad4 OTH exome
AF:
0.638
GnomAD4 genome
AF:
0.526
AC:
79903
AN:
151930
Hom.:
23703
Cov.:
0
AF XY:
0.522
AC XY:
38747
AN XY:
74242
show subpopulations
Gnomad4 AFR
AF:
0.171
Gnomad4 AMR
AF:
0.501
Gnomad4 ASJ
AF:
0.618
Gnomad4 EAS
AF:
0.533
Gnomad4 SAS
AF:
0.463
Gnomad4 FIN
AF:
0.656
Gnomad4 NFE
AF:
0.723
Gnomad4 OTH
AF:
0.566
Alfa
AF:
0.566
Hom.:
3101
Asia WGS
AF:
0.457
AC:
1593
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Aug 09, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs71265055; hg19: chr12-8374781; COSMIC: COSV56709700; COSMIC: COSV56709700; API