chr1-207720437-C-T

Position:

• chr1-207720437-C-T

Variant summary

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

The NM_175710.2(CR1L):​c.1642+2746C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,970 control chromosomes in the GnomAD database, including 4,682 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 0.23 (4682 hom., cov: 31)
• Consequence: CR1L NM_175710.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CR1L	NM_175710.2	c.1642+2746C>T		intron_variant		ENST00000508064.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CR1L	ENST00000508064.7	c.1642+2746C>T		intron_variant		1	NM_175710.2	P1
CR1L	ENST00000294997.10	c.*307+2746C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35417 AN: 151852 Hom.: 4675 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.00693

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.233 AC: 35432 AN: 151970 Hom.: 4682 Cov.: 31 AF XY: 0.232 AC XY: 17211 AN XY: 74294

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.00676

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.212

Alfa AF: 0.278 Hom.: 11574

Bravo AF: 0.229

Asia WGS AF: 0.0830 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
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: rs2761424; hg19: chr1-207893782;