8-8022897-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001423530.1(FAM90A24):​c.102G>A​(p.Pro34Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.000062 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FAM90A24
NM_001423530.1 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.07
Variant links:
Genes affected
FAM90A24P (HGNC:32272): (family with sequence similarity 90 member A24)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
Variant 8-8022897-C-T is Benign according to our data. Variant chr8-8022897-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3771930.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM90A24NM_001423530.1 linkc.102G>A p.Pro34Pro synonymous_variant Exon 1 of 4 NP_001410459.1
LOC124901865 n.8022897C>T intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM90A24PENST00000520792.5 linkc.102G>A p.Pro34Pro synonymous_variant Exon 3 of 6 6 ENSP00000514267.1 P0C7X0

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000617
AC:
1
AN:
16216
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
8162
show subpopulations
Gnomad4 AFR exome
AF:
0.000429
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

ClinVar

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

Submissions by phenotype

not provided Benign:1
Jan 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

FAM90A24: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
12
DANN
Benign
0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-7880419; API