rs1874014

Positions:

• chr16-84821910-A-C

Variant summary

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

The NM_031476.4(CRISPLD2):​c.-75+1777A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,058 control chromosomes in the GnomAD database, including 13,800 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 0.42 (13800 hom., cov: 33)
• Consequence: CRISPLD2 NM_031476.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRISPLD2	NM_031476.4	c.-75+1777A>C		intron_variant		ENST00000262424.10	NP_113664.1
CRISPLD2	XM_005256190.2	c.-334+1777A>C		intron_variant			XP_005256247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.-75+1777A>C		intron_variant		1	NM_031476.4	ENSP00000262424.5

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63944 AN: 151940 Hom.: 13791 Cov.: 33

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.421 AC: 63972 AN: 152058 Hom.: 13800 Cov.: 33 AF XY: 0.419 AC XY: 31123 AN XY: 74328

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.435

Alfa AF: 0.408 Hom.: 21968

Bravo AF: 0.419

Asia WGS AF: 0.329 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.51

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: rs1874014; hg19: chr16-84855516;