1-207322082-G-T

Position:

• chr1-207322082-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000367064.9(CD55):​c.100+217G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,994 control chromosomes in the GnomAD database, including 12,629 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 0.40 (12629 hom., cov: 32)
• Consequence: CD55 ENST00000367064.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

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]

LOC107985251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD55	NM_000574.5	c.100+217G>T		intron_variant		ENST00000367064.9	NP_000565.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD55	ENST00000367064.9	c.100+217G>T		intron_variant		1	NM_000574.5	ENSP00000356031.4

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60704 AN: 151876 Hom.: 12615 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.400 AC: 60742 AN: 151994 Hom.: 12629 Cov.: 32 AF XY: 0.400 AC XY: 29684 AN XY: 74294

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.451

Alfa AF: 0.299 Hom.: 976

Bravo AF: 0.397

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.59

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: rs7533852; hg19: chr1-207495427; COSMIC: COSV58577126; COSMIC: COSV58577126;