Genetic Variant NM_175710.2:c.1328+212G>T (chr1-207701830-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

27 publications found

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:

ENSG00000308069 (HGNC:):

ENSG00000308069 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175710.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CR1L	NM_175710.2	MANE Select	c.1328+212G>T		intron	N/A	NP_783641.1	Q2VPA4-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CR1L	ENST00000508064.7	TSL:1 MANE Select	c.1328+212G>T	intron	N/A	ENSP00000421736.2	Q2VPA4-1
CR1L	ENST00000294997.10	TSL:1	n.1160+212G>T	intron	N/A	ENSP00000434864.1	A0A0C4DGF5
CR1L	ENST00000530905.1	TSL:5	n.494-8552G>T	intron	N/A

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

African (AFR)

AF:

0.268

AC:

4401

AN:

16422

American (AMR)

AF:

0.474

AC:

16156

AN:

34100

Ashkenazi Jewish (ASJ)

AF:

0.203

AC:

4009

AN:

19750

East Asian (EAS)

AF:

0.359

AC:

11119

AN:

30972

South Asian (SAS)

AF:

0.335

AC:

21131

AN:

63040

European-Finnish (FIN)

AF:

0.317

AC:

14693

AN:

46282

Middle Eastern (MID)

AF:

0.214

AC:

781

AN:

3654

European-Non Finnish (NFE)

AF:

0.252

AC:

92264

AN:

365564

Other (OTH)

AF:

0.269

AC:

8480

AN:

31578

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

6532

13065

19597

26130

32662

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1212

2424

3636

4848

6060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.283

AC:

43059

AN:

151966

Hom.:

6450

Cov.:

AF XY:

0.292

AC XY:

21684

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.265

AC:

10995

AN:

41460

American (AMR)

AF:

0.431

AC:

6560

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.218

AC:

754

AN:

3464

East Asian (EAS)

AF:

0.327

AC:

1685

AN:

5158

South Asian (SAS)

AF:

0.326

AC:

1569

AN:

4820

European-Finnish (FIN)

AF:

0.317

AC:

3345

AN:

10542

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.252

AC:

17158

AN:

67970

Other (OTH)

AF:

0.292

AC:

617

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1534

3068

4602

6136

7670

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

438

876

1314

1752

2190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.263

Hom.:

20345

Bravo

AF:

0.292

Asia WGS

AF:

0.302

AC:

1051

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.6

(source)

DANN

Benign

0.78

PhyloP100

0.28

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over