rs4782675

chr16-84854704-C-T

Variant summary

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

The NM_031476.4(CRISPLD2):c.609-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,577,338 control chromosomes in the GnomAD database, including 43,121 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 0.21 (3659 hom., cov: 32)
  • Exomes 𝑓: 0.23 (39462 hom.)
• Consequence: CRISPLD2 NM_031476.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRISPLD2	NM_031476.4	c.609-25C>T		intron_variant		ENST00000262424.10
CRISPLD2	XM_005256190.2	c.609-25C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.609-25C>T		intron_variant		1	NM_031476.4	P4
	ENST00000648152.1	n.372+1590G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31880 AN: 151946 Hom.: 3655 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.207

GnomAD3 exomes AF: 0.230 AC: 57289 AN: 249394 Hom.: 7668 AF XY: 0.232 AC XY: 31296 AN XY: 134898

Gnomad AFR exome AF: 0.159

Gnomad AMR exome AF: 0.141

Gnomad ASJ exome AF: 0.264

Gnomad EAS exome AF: 0.518

Gnomad SAS exome AF: 0.225

Gnomad FIN exome AF: 0.178

Gnomad NFE exome AF: 0.228

Gnomad OTH exome AF: 0.228

GnomAD4 exome AF: 0.229 AC: 326494 AN: 1425274 Hom.: 39462 Cov.: 26 AF XY: 0.230 AC XY: 163457 AN XY: 711324

Gnomad4 AFR exome AF: 0.162

Gnomad4 AMR exome AF: 0.144

Gnomad4 ASJ exome AF: 0.265

Gnomad4 EAS exome AF: 0.478

Gnomad4 SAS exome AF: 0.226

Gnomad4 FIN exome AF: 0.178

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.238

GnomAD4 genome AF: 0.210 AC: 31898 AN: 152064 Hom.: 3659 Cov.: 32 AF XY: 0.208 AC XY: 15433 AN XY: 74360

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.211

Alfa AF: 0.225 Hom.: 2042

Bravo AF: 0.213

Asia WGS AF: 0.320 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.017
Dann	Benign	0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs4782675; hg19: chr16-84888310;