16-84838445-G-C

Position:

• chr16-84838445-G-C

Variant summary

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

The NM_031476.4(CRISPLD2):​c.-51G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 1,584,088 control chromosomes in the GnomAD database, including 366,443 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 0.69 (36984 hom., cov: 33)
  • Exomes 𝑓: 0.68 (329459 hom.)
• Consequence: CRISPLD2 NM_031476.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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]

CRISPLD2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRISPLD2	NM_031476.4	c.-51G>C		5_prime_UTR_variant	2/15	ENST00000262424.10	NP_113664.1
CRISPLD2	XM_005256190.2	c.-51G>C		5_prime_UTR_variant	3/16		XP_005256247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.-51G>C		5_prime_UTR_variant	2/15	1	NM_031476.4	ENSP00000262424.5

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105462 AN: 151960 Hom.: 36953 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.677

GnomAD3 exomes AF: 0.668 AC: 155429 AN: 232544 Hom.: 52736 AF XY: 0.668 AC XY: 83277 AN XY: 124706

Gnomad AFR exome AF: 0.750

Gnomad AMR exome AF: 0.683

Gnomad ASJ exome AF: 0.658

Gnomad EAS exome AF: 0.412

Gnomad SAS exome AF: 0.686

Gnomad FIN exome AF: 0.734

Gnomad NFE exome AF: 0.680

Gnomad OTH exome AF: 0.663

GnomAD4 exome AF: 0.676 AC: 968609 AN: 1432010 Hom.: 329459 Cov.: 39 AF XY: 0.676 AC XY: 478859 AN XY: 708480

Gnomad4 AFR exome AF: 0.751

Gnomad4 AMR exome AF: 0.685

Gnomad4 ASJ exome AF: 0.662

Gnomad4 EAS exome AF: 0.463

Gnomad4 SAS exome AF: 0.690

Gnomad4 FIN exome AF: 0.731

Gnomad4 NFE exome AF: 0.679

Gnomad4 OTH exome AF: 0.662

GnomAD4 genome AF: 0.694 AC: 105550 AN: 152078 Hom.: 36984 Cov.: 33 AF XY: 0.695 AC XY: 51637 AN XY: 74344

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.680

Alfa AF: 0.633 Hom.: 3285

Bravo AF: 0.687

Asia WGS AF: 0.602 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1546124; hg19: chr16-84872051; COSMIC: COSV52278536; COSMIC: COSV52278536;