1-207658012-C-G

Position:

• chr1-207658012-C-G

Variant summary

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

The NM_175710.2(CR1L):​c.97+12682C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,940 control chromosomes in the GnomAD database, including 10,187 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 0.36 (10187 hom., cov: 32)
• Consequence: CR1L NM_175710.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CR1L	NM_175710.2	c.97+12682C>G		intron_variant		ENST00000508064.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CR1L	ENST00000508064.7	c.97+12682C>G		intron_variant		1	NM_175710.2	P1
CR1L	ENST00000531844.5	n.218+12682C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55168 AN: 151820 Hom.: 10188 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.363 AC: 55190 AN: 151940 Hom.: 10187 Cov.: 32 AF XY: 0.359 AC XY: 26625 AN XY: 74248

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.364

Alfa AF: 0.233 Hom.: 537

Bravo AF: 0.362

Asia WGS AF: 0.369 AC: 1281 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.53

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: rs11118278; hg19: chr1-207831357; COSMIC: COSV71448827; COSMIC: COSV71448827;