chr9-86266085-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_030940.4(ISCA1):c.348C>T(p.Asn116=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0237 in 1,612,782 control chromosomes in the GnomAD database, including 570 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 53 hom., cov: 32)
Exomes 𝑓: 0.024 ( 517 hom. )
Consequence
ISCA1
NM_030940.4 synonymous
NM_030940.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.64
Genes affected
ISCA1 (HGNC:28660): (iron-sulfur cluster assembly 1) ISCA1 is a mitochondrial protein involved in the biogenesis and assembly of iron-sulfur clusters, which play a role in electron-transfer reactions (Cozar-Castellano et al., 2004 [PubMed 15262227]).[supplied by OMIM, Mar 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
Variant 9-86266085-G-A is Benign according to our data. Variant chr9-86266085-G-A is described in ClinVar as [Benign]. Clinvar id is 1169189.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.018 (2738/152296) while in subpopulation NFE AF= 0.0259 (1764/68014). AF 95% confidence interval is 0.0249. There are 53 homozygotes in gnomad4. There are 1239 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 53 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISCA1 | NM_030940.4 | c.348C>T | p.Asn116= | synonymous_variant | 4/4 | ENST00000375991.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISCA1 | ENST00000375991.9 | c.348C>T | p.Asn116= | synonymous_variant | 4/4 | 1 | NM_030940.4 | P1 | |
ISCA1 | ENST00000311534.6 | c.54C>T | p.Asn18= | synonymous_variant | 4/4 | 2 | |||
ISCA1 | ENST00000637705.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0180 AC: 2735AN: 152178Hom.: 53 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
2735
AN:
152178
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0193 AC: 4742AN: 245338Hom.: 77 AF XY: 0.0197 AC XY: 2623AN XY: 132934
GnomAD3 exomes
AF:
AC:
4742
AN:
245338
Hom.:
AF XY:
AC XY:
2623
AN XY:
132934
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0243 AC: 35453AN: 1460486Hom.: 517 Cov.: 31 AF XY: 0.0241 AC XY: 17528AN XY: 726516
GnomAD4 exome
AF:
AC:
35453
AN:
1460486
Hom.:
Cov.:
31
AF XY:
AC XY:
17528
AN XY:
726516
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0180 AC: 2738AN: 152296Hom.: 53 Cov.: 32 AF XY: 0.0166 AC XY: 1239AN XY: 74486
GnomAD4 genome
?
AF:
AC:
2738
AN:
152296
Hom.:
Cov.:
32
AF XY:
AC XY:
1239
AN XY:
74486
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at