Genetic Variant NM_000562.3:c.1455C>T (chr1-56912477-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000562.3(C8A):c.1455C>T(p.Arg485Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 1,614,082 control chromosomes in the GnomAD database, including 4,779 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1237 hom., cov: 33)

Exomes 𝑓: 0.058 ( 3542 hom. )

Consequence

C8A
NM_000562.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0140

Variant links:

Genes affected

C8A (HGNC:1352): (complement C8 alpha chain) C8 is a component of the complement system and contains three polypeptides, alpha, beta and gamma. This gene encodes the alpha subunit of C8. C8 participates in the formation of the membrane attack complex (MAC). The MAC assembles on bacterial membranes to form a pore, permitting disruption of bacterial membrane organization. Mutations in this gene cause complement C8 alpha-gamma deficiency. [provided by RefSeq, Nov 2008]

C8A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 1-56912477-C-T is Benign according to our data. Variant chr1-56912477-C-T is described in ClinVar as [Benign]. Clinvar id is 402462.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.014 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C8A	NM_000562.3 link	c.1455C>T	p.Arg485Arg	synonymous_variant	Exon 10 of 11	ENST00000361249.4	NP_000553.1	P07357

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C8A	ENST00000361249.4 link	c.1455C>T	p.Arg485Arg	synonymous_variant	Exon 10 of 11	1	NM_000562.3	ENSP00000354458.3		P07357

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15577

AN:

152120

Hom.:

1235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.0415

Gnomad EAS

AF:

0.0517

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.0470

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0459

Gnomad OTH

AF:

0.104

GnomAD3 exomes

AF:

0.0756

AC:

19007

AN:

251306

Hom.:

1071

AF XY:

0.0752

AC XY:

10218

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.225

Gnomad AMR exome

AF:

0.0917

Gnomad ASJ exome

AF:

0.0454

Gnomad EAS exome

AF:

0.0518

Gnomad SAS exome

AF:

0.134

Gnomad FIN exome

AF:

0.0483

Gnomad NFE exome

AF:

0.0456

Gnomad OTH exome

AF:

0.0711

GnomAD4 exome

AF:

0.0581

AC:

84892

AN:

1461844

Hom.:

3542

Cov.:

AF XY:

0.0598

AC XY:

43481

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.228

Gnomad4 AMR exome

AF:

0.0928

Gnomad4 ASJ exome

AF:

0.0431

Gnomad4 EAS exome

AF:

0.0650

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.0459

Gnomad4 NFE exome

AF:

0.0457

Gnomad4 OTH exome

AF:

0.0681

GnomAD4 genome

AF:

0.102

AC:

15599

AN:

152238

Hom.:

1237

Cov.:

AF XY:

0.102

AC XY:

7597

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.0415

Gnomad4 EAS

AF:

0.0517

Gnomad4 SAS

AF:

0.139

Gnomad4 FIN

AF:

0.0470

Gnomad4 NFE

AF:

0.0459

Gnomad4 OTH

AF:

0.102

Alfa

AF:

0.0665

Hom.:

286

Bravo

AF:

0.110

Asia WGS

AF:

0.107

AC:

374

AN:

3478

EpiCase

AF:

0.0480

EpiControl

AF:

0.0511

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

3.5

DANN

Benign

0.40

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.

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