rs6700079

Variant names:

• chr1-207328527-T-C
• rs6700079
• NM_000574.5:c.664+1690T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-207328527-T-C
• chr1-207328527-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000574.5(CD55):​c.664+1690T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 151,942 control chromosomes in the GnomAD database, including 36,787 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 0.69 (36787 hom., cov: 32)
• Consequence: CD55 NM_000574.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 8 publications found

Genes affected

CD55 (HGNC:2665): (CD55 molecule (Cromer blood group)) This gene encodes a glycoprotein involved in the regulation of the complement cascade. Binding of the encoded protein to complement proteins accelerates their decay, thereby disrupting the cascade and preventing damage to host cells. Antigens present on this protein constitute the Cromer blood group system (CROM). Alternative splicing results in multiple transcript variants. The predominant transcript variant encodes a membrane-bound protein, but alternatively spliced transcripts may produce soluble proteins. [provided by RefSeq, Jul 2014]

CD55 Gene-Disease associations (from GenCC):

• protein-losing enteropathy

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000574.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD55	NM_000574.5	MANE Select	c.664+1690T>C		intron	N/A	NP_000565.1	P08174-1
	CD55	NM_001300902.2		c.664+1690T>C		intron	N/A	NP_001287831.1	B1AP13
	CD55	NM_001114752.3		c.664+1690T>C		intron	N/A	NP_001108224.1	P08174-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD55	ENST00000367064.9	TSL:1 MANE Select	c.664+1690T>C		intron	N/A	ENSP00000356031.4	P08174-1
	CD55	ENST00000367063.6	TSL:1	c.664+1690T>C		intron	N/A	ENSP00000356030.2	B1AP13
	CD55	ENST00000314754.12	TSL:1	c.664+1690T>C		intron	N/A	ENSP00000316333.8	P08174-2

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104985 AN: 151824 Hom.: 36753 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.692 AC: 105078 AN: 151942 Hom.: 36787 Cov.: 32 AF XY: 0.688 AC XY: 51107 AN XY: 74274

African (AFR) AF: 0.683 AC: 28334 AN: 41466

American (AMR) AF: 0.694 AC: 10593 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2976 AN: 3464

East Asian (EAS) AF: 0.422 AC: 2174 AN: 5150

South Asian (SAS) AF: 0.573 AC: 2767 AN: 4826

European-Finnish (FIN) AF: 0.751 AC: 7924 AN: 10552

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47783 AN: 67904

Other (OTH) AF: 0.730 AC: 1544 AN: 2114

Alfa AF: 0.702 Hom.: 4665

Bravo AF: 0.689

Asia WGS AF: 0.477 AC: 1665 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.58
PhyloP100		0.039
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6700079; hg19: chr1-207501872;