rs774206

Positions:

• chr16-84886352-A-G
• chr16-84886352-A-T

Variant summary

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

The NM_031476.4(CRISPLD2):​c.1306-2878A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,048 control chromosomes in the GnomAD database, including 12,311 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 0.39 (12311 hom., cov: 32)
• Consequence: CRISPLD2 NM_031476.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.865

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRISPLD2	NM_031476.4	c.1306-2878A>G		intron_variant		ENST00000262424.10
CRISPLD2	XM_005256190.2	c.1306-2878A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.1306-2878A>G		intron_variant		1	NM_031476.4	P4
CRISPLD2	ENST00000567845.5	c.1303-2878A>G		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59424 AN: 151930 Hom.: 12303 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.391 AC: 59459 AN: 152048 Hom.: 12311 Cov.: 32 AF XY: 0.389 AC XY: 28948 AN XY: 74328

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.404

Alfa AF: 0.353 Hom.: 5309

Bravo AF: 0.398

Asia WGS AF: 0.476 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.62

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: rs774206; hg19: chr16-84919958;