rs4783099

chr16-84907723-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.*1081C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,066 control chromosomes in the GnomAD database, including 10,585 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 (10584 hom., cov: 32)
  • Exomes 𝑓: 0.24 (1 hom.)
• Consequence: CRISPLD2 NM_031476.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRISPLD2	NM_031476.4	c.*1081C>T		3_prime_UTR_variant	15/15	ENST00000262424.10
CRISPLD2	XM_005256190.2	c.*1081C>T		3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.*1081C>T		3_prime_UTR_variant	15/15	1	NM_031476.4	P4
CRISPLD2	ENST00000566165.1	c.121-11917C>T		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56214 AN: 151912 Hom.: 10588 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.360

GnomAD4 exome AF: 0.235 AC: 8 AN: 34 Hom.: 1 Cov.: 0 AF XY: 0.154 AC XY: 4 AN XY: 26

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.273

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.370 AC: 56235 AN: 152032 Hom.: 10584 Cov.: 32 AF XY: 0.371 AC XY: 27585 AN XY: 74304

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.361

Alfa AF: 0.363 Hom.: 9987

Bravo AF: 0.375

Asia WGS AF: 0.433 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.15
Dann	Benign	0.79

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: rs4783099; hg19: chr16-84941329;