Genetic Variant CRISPLD2:c.*2390T>G (chr16-84909032-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031476.4(CRISPLD2):c.*2390T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,092 control chromosomes in the GnomAD database, including 5,231 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 0.25 ( 5230 hom., cov: 31)

Exomes 𝑓: 0.20 ( 1 hom. )

Consequence

CRISPLD2
NM_031476.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750

Publications

15 publications found

Variant links:

Genes affected

CRISPLD2 (HGNC:25248): (cysteine rich secretory protein LCCL domain containing 2) Predicted to enable glycosaminoglycan binding activity. Involved in face morphogenesis. Located in transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

CRISPLD2 links:

ENSG00000279622 (HGNC:):

ENSG00000279622 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=-0.72).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRISPLD2	NM_031476.4 link	c.*2390T>G		3_prime_UTR_variant	Exon 15 of 15	ENST00000262424.10	NP_113664.1
CRISPLD2	XM_005256190.2 link	c.*2390T>G		3_prime_UTR_variant	Exon 16 of 16		XP_005256247.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
CRISPLD2	ENST00000262424.10 link	c.*2390T>G	3_prime_UTR_variant	Exon 15 of 15	1	NM_031476.4	ENSP00000262424.5
CRISPLD2	ENST00000566165.1 link	n.120-10608T>G	intron_variant	Intron 1 of 2	3		ENSP00000463171.1
ENSG00000279622	ENST00000741212.1 link	n.221+14511A>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38408

AN:

151934

Hom.:

5234

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.233

Gnomad EAS

AF:

0.225

Gnomad SAS

AF:

0.340

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.220

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.269

GnomAD4 exome

AF:

0.200

AC:

AN:

Hom.:

Cov.:

AF XY:

0.233

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.222

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.253

AC:

38409

AN:

152052

Hom.:

5230

Cov.:

AF XY:

0.256

AC XY:

19002

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.159

AC:

6596

AN:

41480

American (AMR)

AF:

0.321

AC:

4888

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

807

AN:

3464

East Asian (EAS)

AF:

0.224

AC:

1162

AN:

5182

South Asian (SAS)

AF:

0.340

AC:

1638

AN:

4818

European-Finnish (FIN)

AF:

0.272

AC:

2867

AN:

10556

Middle Eastern (MID)

AF:

0.226

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.289

AC:

19625

AN:

67990

Other (OTH)

AF:

0.266

AC:

560

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1423

2846

4270

5693

7116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<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:

0.216

Hom.:

1856

Bravo

AF:

0.252

Asia WGS

AF:

0.274

AC:

956

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

9.1

(source)

DANN

Benign

0.75

PhyloP100

-0.075

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over