rs28371583

Variant names:

• chr1-207321334-A-G
• rs28371583
• XR_007066837.1:n.444+352T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-207321334-A-G
• chr1-207321334-A-T

Variant summary

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

The XR_007066837.1(LOC107985251):​n.444+352T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 159,474 control chromosomes in the GnomAD database, including 7,406 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 0.30 (7165 hom., cov: 33)
  • Exomes 𝑓: 0.24 (241 hom.)
• Consequence: LOC107985251 XR_007066837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

Genes affected

LOC107985251 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985251	XR_007066837.1	n.444+352T>C		intron_variant	Intron 1 of 3
LOC107985251	XR_007066838.1	n.444+352T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD55	ENST00000367063.6	c.-432A>G		upstream_gene_variant		1		ENSP00000356030.2
CD55	ENST00000695824.1	c.-432A>G		upstream_gene_variant				ENSP00000512201.1
CD55	ENST00000695828.1	c.-432A>G		upstream_gene_variant				ENSP00000512204.1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45008 AN: 152008 Hom.: 7158 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.278

GnomAD4 exome AF: 0.238 AC: 1752 AN: 7348 Hom.: 241 Cov.: 0 AF XY: 0.230 AC XY: 878 AN XY: 3816

Gnomad4 AFR exome AF: 0.418

Gnomad4 AMR exome AF: 0.195

Gnomad4 ASJ exome AF: 0.366

Gnomad4 EAS exome AF: 0.0565

Gnomad4 SAS exome AF: 0.192

Gnomad4 FIN exome AF: 0.267

Gnomad4 NFE exome AF: 0.240

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.296 AC: 45052 AN: 152126 Hom.: 7165 Cov.: 33 AF XY: 0.293 AC XY: 21767 AN XY: 74348

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0555

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.276

Alfa AF: 0.305 Hom.: 1206

Bravo AF: 0.296

Asia WGS AF: 0.138 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28371583; hg19: chr1-207494679;