chr16-84886352-A-G

Variant names:

• chr16-84886352-A-G
• rs774206
• NM_031476.4:c.1306-2878A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031476.4. 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
	CRISPLD2	NM_031476.4	MANE Select	c.1306-2878A>G		intron	N/A	NP_113664.1	Q9H0B8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD2	ENST00000262424.10	TSL:1 MANE Select	c.1306-2878A>G		intron	N/A	ENSP00000262424.5	Q9H0B8-1
	CRISPLD2	ENST00000941702.1		c.1306-2878A>G		intron	N/A	ENSP00000611761.1
	CRISPLD2	ENST00000941703.1		c.1306-2878A>G		intron	N/A	ENSP00000611762.1

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

African (AFR) AF: 0.494 AC: 20493 AN: 41474

American (AMR) AF: 0.317 AC: 4839 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3398 AN: 5162

South Asian (SAS) AF: 0.412 AC: 1986 AN: 4820

European-Finnish (FIN) AF: 0.282 AC: 2984 AN: 10578

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23369 AN: 67956

Other (OTH) AF: 0.404 AC: 849 AN: 2104

Alfa AF: 0.353 Hom.: 7159

Bravo AF: 0.398

Asia WGS AF: 0.476 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		0.86
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs774206; hg19: chr16-84919958;