16-84869111-A-G

Variant summary

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

The NM_031476.4(CRISPLD2):c.914+200A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,130 control chromosomes in the GnomAD database, including 11,118 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 0.37 (11118 hom., cov: 33)
• Consequence: CRISPLD2 NM_031476.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRISPLD2	NM_031476.4	c.914+200A>G		intron_variant		ENST00000262424.10
CRISPLD2	XM_005256190.2	c.914+200A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.914+200A>G		intron_variant		1	NM_031476.4	P4

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56629 AN: 152012 Hom.: 11105 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.373 AC: 56679 AN: 152130 Hom.: 11118 Cov.: 33 AF XY: 0.373 AC XY: 27729 AN XY: 74372

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.397

Alfa AF: 0.338 Hom.: 18704

Bravo AF: 0.378

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.55

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: rs2326398; hg19: chr16-84902717;