1-207113842-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000715.4(C4BPA):c.143-258C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,854 control chromosomes in the GnomAD database, including 13,569 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (13569 hom., cov: 31)
• Consequence: C4BPA NM_000715.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.55

Genes affected

C4BPA (HGNC:1325): (complement component 4 binding protein alpha) This gene encodes a member of a superfamily of proteins composed predominantly of tandemly arrayed short consensus repeats of approximately 60 amino acids. Along with a single, unique beta-chain, seven identical alpha-chains encoded by this gene assemble into the predominant isoform of C4b-binding protein, a multimeric protein that controls activation of the complement cascade through the classical pathway. The genes encoding both alpha and beta chains are located adjacent to each other on human chromosome 1 in the regulator of complement activation gene cluster. Two pseudogenes of this gene are also found in the cluster. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 1-207113842-C-T is Benign according to our data. Variant chr1-207113842-C-T is described in ClinVar as [Benign]. Clinvar id is 1267035.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C4BPA	NM_000715.4	c.143-258C>T		intron_variant		ENST00000367070.8
C4BPA	XM_005273251.3	c.143-258C>T		intron_variant
C4BPA	XM_005273252.5	c.143-258C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C4BPA	ENST00000367070.8	c.143-258C>T		intron_variant		1	NM_000715.4	P1
C4BPA	ENST00000421786.5	c.143-258C>T		intron_variant		4
C4BPA	ENST00000424088.1	c.143-258C>T		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52151 AN: 151740 Hom.: 13532 Cov.: 31

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.333

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.344 AC: 52240 AN: 151854 Hom.: 13569 Cov.: 31 AF XY: 0.337 AC XY: 25030 AN XY: 74250

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.329

Alfa AF: 0.204 Hom.: 5717

Bravo AF: 0.372

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.045
Dann	Benign	0.45

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

Other links and lift over

dbSNP: rs2808470; hg19: chr1-207287187; COSMIC: COSV65536007;