Variant chr7-25121995-A-ATGTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018947.6(CYCS):c.*1705_*1706insAACA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.40 ( 12718 hom., cov: 0)

Exomes 𝑓: 0.17 ( 0 hom. )

Consequence

CYCS
NM_018947.6 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.379

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]

CYCS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-25121995-A-ATGTT is Benign according to our data. Variant chr7-25121995-A-ATGTT is described in ClinVar as [Likely_benign]. Clinvar id is 359923.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYCS	NM_018947.6 linkuse as main transcript	c.1705_1706insAACA		3_prime_UTR_variant	3/3	ENST00000305786.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYCS	ENST00000305786.7 linkuse as main transcript	c.1705_1706insAACA		3_prime_UTR_variant	3/3	1	NM_018947.6	P1

Frequencies

GnomAD3 genomes

AF:

0.397

AC:

59234

AN:

149116

Hom.:

12685

Cov.:

show subpopulations

Gnomad AFR

AF:

0.571

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.537

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.314

Gnomad OTH

AF:

0.387

GnomAD4 exome

AF:

0.167

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.398

AC:

59322

AN:

149232

Hom.:

12718

Cov.:

AF XY:

0.396

AC XY:

28816

AN XY:

72686

show subpopulations

Gnomad4 AFR

AF:

0.571

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.348

Gnomad4 EAS

AF:

0.538

Gnomad4 SAS

AF:

0.346

Gnomad4 FIN

AF:

0.255

Gnomad4 NFE

AF:

0.314

Gnomad4 OTH

AF:

0.393

Alfa

AF:

0.333

Hom.:

906

Asia WGS

AF:

0.477

AC:

1660

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Thrombocytopenia

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over