rs1861525

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_018947.6(CYCS):​c.*1718T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0318 in 126,080 control chromosomes in the GnomAD database, including 71 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.032 ( 71 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CYCS
NM_018947.6 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.338
Variant links:
Genes affected
CYCS (HGNC:19986): (cytochrome c, somatic) This gene encodes a small heme protein that functions as a central component of the electron transport chain in mitochondria. The encoded protein associates with the inner membrane of the mitochondrion where it accepts electrons from cytochrome b and transfers them to the cytochrome oxidase complex. This protein is also involved in initiation of apoptosis. Mutations in this gene are associated with autosomal dominant nonsyndromic thrombocytopenia. Numerous processed pseudogenes of this gene are found throughout the human genome.[provided by RefSeq, Jul 2010]

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=-0.89).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0318 (4013/126080) while in subpopulation NFE AF= 0.0438 (2738/62488). AF 95% confidence interval is 0.0424. There are 71 homozygotes in gnomad4. There are 1850 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 4013 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYCSNM_018947.6 linkuse as main transcriptc.*1718T>C 3_prime_UTR_variant 3/3 ENST00000305786.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYCSENST00000305786.7 linkuse as main transcriptc.*1718T>C 3_prime_UTR_variant 3/31 NM_018947.6 P1

Frequencies

GnomAD3 genomes
AF:
0.0318
AC:
4013
AN:
126016
Hom.:
71
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0118
Gnomad AMI
AF:
0.0278
Gnomad AMR
AF:
0.0382
Gnomad ASJ
AF:
0.0666
Gnomad EAS
AF:
0.000263
Gnomad SAS
AF:
0.0167
Gnomad FIN
AF:
0.00929
Gnomad MID
AF:
0.0310
Gnomad NFE
AF:
0.0438
Gnomad OTH
AF:
0.0366
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
12
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
10
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.0318
AC:
4013
AN:
126080
Hom.:
71
Cov.:
32
AF XY:
0.0302
AC XY:
1850
AN XY:
61164
show subpopulations
Gnomad4 AFR
AF:
0.0118
Gnomad4 AMR
AF:
0.0382
Gnomad4 ASJ
AF:
0.0666
Gnomad4 EAS
AF:
0.000263
Gnomad4 SAS
AF:
0.0169
Gnomad4 FIN
AF:
0.00929
Gnomad4 NFE
AF:
0.0438
Gnomad4 OTH
AF:
0.0363
Alfa
AF:
0.0404
Hom.:
185
Bravo
AF:
0.0274
Asia WGS
AF:
0.00809
AC:
29
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.2
DANN
Benign
0.55

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: rs1861525; hg19: chr7-25161602; API