Genetic Variant CR1L:c.1328+212G>T (chr1-207701830-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.278

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt
CR1L	NM_175710.2 link	c.1328+212G>T		intron_variant	Intron 9 of 11	ENST00000508064.7	NP_783641.1	Q2VPA4-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CR1L	ENST00000508064.7 link	c.1328+212G>T	intron_variant	Intron 9 of 11	1	NM_175710.2	ENSP00000421736.2	Q2VPA4-1
CR1L	ENST00000294997.10 link	n.1160+212G>T	intron_variant	Intron 8 of 12	1		ENSP00000434864.1	A0A0C4DGF5
CR1L	ENST00000530905.1 link	n.494-8552G>T	intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.283

AC:

43015

AN:

151848

Hom.:

6434

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.292

AC XY:

21684

AN XY:

74254

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over