19-36151660-AC-ACCCCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001864.4(COX7A1):​c.102+5_102+8dupGGGG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 144,030 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0020 ( 0 hom., cov: 32)

Consequence

COX7A1
NM_001864.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0720
Variant links:
Genes affected
COX7A1 (HGNC:2287): (cytochrome c oxidase subunit 7A1) Cytochrome c oxidase (COX), the terminal component of the mitochondrial respiratory chain, catalyzes the electron transfer from reduced cytochrome c to oxygen. This component is a heteromeric complex consisting of 3 catalytic subunits encoded by mitochondrial genes and multiple structural subunits encoded by nuclear genes. The mitochondrially-encoded subunits function in electron transfer, and the nuclear-encoded subunits may function in the regulation and assembly of the complex. This nuclear gene encodes polypeptide 1 (muscle isoform) of subunit VIIa and the polypeptide 1 is present only in muscle tissues. Other polypeptides of subunit VIIa are present in both muscle and nonmuscle tissues, and are encoded by different genes. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COX7A1NM_001864.4 linkc.102+5_102+8dupGGGG splice_region_variant, intron_variant Intron 2 of 3 ENST00000292907.8 NP_001855.1 P24310Q6FGI7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COX7A1ENST00000292907.8 linkc.102+5_102+8dupGGGG splice_region_variant, intron_variant Intron 2 of 3 1 NM_001864.4 ENSP00000292907.3 P24310
COX7A1ENST00000589154.1 linkc.75+32_75+35dupGGGG intron_variant Intron 2 of 3 5 ENSP00000468063.3 K7ER11
COX7A1ENST00000437291.6 linkc.-67+5_-67+8dupGGGG splice_region_variant, intron_variant Intron 2 of 3 3 ENSP00000475885.1 U3KQH8
COX7A1ENST00000481297.1 linkn.149_152dupGGGG non_coding_transcript_exon_variant Exon 2 of 3 2

Frequencies

GnomAD3 genomes
AF:
0.00202
AC:
291
AN:
143914
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00256
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00174
Gnomad ASJ
AF:
0.00238
Gnomad EAS
AF:
0.000642
Gnomad SAS
AF:
0.000223
Gnomad FIN
AF:
0.00365
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00177
Gnomad OTH
AF:
0.00205
GnomAD3 exomes
AF:
0.00297
AC:
557
AN:
187824
Hom.:
0
AF XY:
0.00293
AC XY:
302
AN XY:
103144
show subpopulations
Gnomad AFR exome
AF:
0.00118
Gnomad AMR exome
AF:
0.00667
Gnomad ASJ exome
AF:
0.00446
Gnomad EAS exome
AF:
0.00358
Gnomad SAS exome
AF:
0.00266
Gnomad FIN exome
AF:
0.00254
Gnomad NFE exome
AF:
0.00186
Gnomad OTH exome
AF:
0.00349
GnomAD4 exome
Cov.:
31
GnomAD4 genome
AF:
0.00202
AC:
291
AN:
144030
Hom.:
0
Cov.:
32
AF XY:
0.00190
AC XY:
133
AN XY:
69966
show subpopulations
Gnomad4 AFR
AF:
0.00255
Gnomad4 AMR
AF:
0.00174
Gnomad4 ASJ
AF:
0.00238
Gnomad4 EAS
AF:
0.000644
Gnomad4 SAS
AF:
0.000223
Gnomad4 FIN
AF:
0.00365
Gnomad4 NFE
AF:
0.00177
Gnomad4 OTH
AF:
0.00203
Alfa
AF:
0.00233
Hom.:
0

ClinVar

Not reported in ClinVar

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: rs3214131; hg19: chr19-36642562; API