1-207698945-T-C

Position:

• chr1-207698945-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

CR1L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CR1L	NM_175710.2	c.1143-244T>C		intron_variant		ENST00000508064.7	NP_783641.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CR1L	ENST00000508064.7	c.1143-244T>C		intron_variant		1	NM_175710.2	ENSP00000421736.2
CR1L	ENST00000294997.10	n.975-244T>C		intron_variant		1		ENSP00000434864.1
CR1L	ENST00000530905.1	n.494-11437T>C		intron_variant		5

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

Gnomad4 AFR AF: 0.0823

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0292

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.202

Alfa AF: 0.244 Hom.: 10820

Bravo AF: 0.178

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.73

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: rs7527798; hg19: chr1-207872290;