16-84911573-G-T

Variant summary

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

The ENST00000566165.1(CRISPLD2):c.121-8067G>T variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 151,942 control chromosomes in the GnomAD database, including 33,979 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 0.67 (33979 hom., cov: 31)
• Consequence: CRISPLD2 ENST00000566165.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD2	ENST00000566165.1	c.121-8067G>T		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101284 AN: 151826 Hom.: 33953 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.667 AC: 101361 AN: 151942 Hom.: 33979 Cov.: 31 AF XY: 0.672 AC XY: 49936 AN XY: 74258

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.672

Alfa AF: 0.638 Hom.: 37792

Bravo AF: 0.666

Asia WGS AF: 0.611 AC: 2126 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	1.0
Dann	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs903194; hg19: chr16-84945179;