1-207701830-G-T

Position:

• chr1-207701830-G-T

Variant summary

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

The NM_175710.2(CR1L):​c.1328+212G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 763,328 control chromosomes in the GnomAD database, including 32,538 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 0.28 (6450 hom., cov: 31)
  • Exomes 𝑓: 0.28 (26088 hom.)
• Consequence: CR1L NM_175710.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CR1L	NM_175710.2	c.1328+212G>T		intron_variant		ENST00000508064.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CR1L	ENST00000508064.7	c.1328+212G>T		intron_variant		1	NM_175710.2	P1
CR1L	ENST00000294997.10	c.1160+212G>T		intron_variant, NMD_transcript_variant		1
CR1L	ENST00000530905.1	n.494-8552G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43015 AN: 151848 Hom.: 6434 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.291

GnomAD4 exome AF: 0.283 AC: 173034 AN: 611362 Hom.: 26088 AF XY: 0.284 AC XY: 92654 AN XY: 326568

Gnomad4 AFR exome AF: 0.268

Gnomad4 AMR exome AF: 0.474

Gnomad4 ASJ exome AF: 0.203

Gnomad4 EAS exome AF: 0.359

Gnomad4 SAS exome AF: 0.335

Gnomad4 FIN exome AF: 0.317

Gnomad4 NFE exome AF: 0.252

Gnomad4 OTH exome AF: 0.269

GnomAD4 genome AF: 0.283 AC: 43059 AN: 151966 Hom.: 6450 Cov.: 31 AF XY: 0.292 AC XY: 21684 AN XY: 74254

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.292

Alfa AF: 0.258 Hom.: 8230

Bravo AF: 0.292

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.78

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: rs4844614; hg19: chr1-207875175; COSMIC: COSV54329836;