rs7527798

Variant names:

• chr1-207698945-T-C
• rs7527798
• NM_175710.2:c.1143-244T>C

Variant summary

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

The NM_175710.2(CR1L):​c.1143-244T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,182 control chromosomes in the GnomAD database, including 3,098 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 0.18 (3098 hom., cov: 32)
• Consequence: CR1L NM_175710.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689
• Publications: 19 publications found

Genes affected

CR1L (HGNC:2335): (complement C3b/C4b receptor 1 like) Acts upstream of or within regulation of complement activation and regulation of complement-dependent cytotoxicity. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000308069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175710.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CR1L	NM_175710.2	MANE Select	c.1143-244T>C		intron	N/A	NP_783641.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CR1L	ENST00000508064.7	TSL:1 MANE Select	c.1143-244T>C		intron	N/A	ENSP00000421736.2
	CR1L	ENST00000294997.10	TSL:1	n.975-244T>C		intron	N/A	ENSP00000434864.1
	CR1L	ENST00000530905.1	TSL:5	n.494-11437T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27881 AN: 152064 Hom.: 3098 Cov.: 32

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0293

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.183 AC: 27885 AN: 152182 Hom.: 3098 Cov.: 32 AF XY: 0.177 AC XY: 13140 AN XY: 74378

African (AFR) AF: 0.0823 AC: 3418 AN: 41532

American (AMR) AF: 0.154 AC: 2358 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3470

East Asian (EAS) AF: 0.0292 AC: 151 AN: 5180

South Asian (SAS) AF: 0.123 AC: 594 AN: 4824

European-Finnish (FIN) AF: 0.190 AC: 2006 AN: 10576

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.265 AC: 17995 AN: 67994

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.233 Hom.: 15734

Bravo AF: 0.178

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.73
PhyloP100		0.69
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: rs7527798; hg19: chr1-207872290;