chr7-25120090-AT-A

Position:

• chr7-25120090-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018947.6(CYCS):​c.*3610del 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 (12508 hom., cov: 0)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: CYCS NM_018947.6 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.36

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-25120090-AT-A is Benign according to our data. Variant chr7-25120090-AT-A is described in ClinVar as [Likely_benign]. Clinvar id is 359886.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYCS	NM_018947.6	c.*3610del		3_prime_UTR_variant	3/3	ENST00000305786.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYCS	ENST00000305786.7	c.*3610del		3_prime_UTR_variant	3/3	1	NM_018947.6	P1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 58084 AN: 145462 Hom.: 12484 Cov.: 0

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.374

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

Gnomad4 NFE exome AF: 0.100

GnomAD4 genome AF: 0.400 AC: 58155 AN: 145522 Hom.: 12508 Cov.: 0 AF XY: 0.396 AC XY: 28075 AN XY: 70834

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.380

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Thrombocytopenia Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60346464; hg19: chr7-25159709;