rs1874015

Positions:

• chr16-84843926-T-C
• chr16-84843926-T-G

Variant summary

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

The NM_031476.4(CRISPLD2):​c.241-1860T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,132 control chromosomes in the GnomAD database, including 40,314 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 0.73 (40314 hom., cov: 32)
• Consequence: CRISPLD2 NM_031476.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRISPLD2	NM_031476.4	c.241-1860T>C		intron_variant		ENST00000262424.10	NP_113664.1
CRISPLD2	XM_005256190.2	c.241-1860T>C		intron_variant			XP_005256247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.241-1860T>C		intron_variant		1	NM_031476.4	ENSP00000262424	P4
	ENST00000648152.1	n.856+1142A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110492 AN: 152014 Hom.: 40260 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.727 AC: 110604 AN: 152132 Hom.: 40314 Cov.: 32 AF XY: 0.728 AC XY: 54166 AN XY: 74368

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.713

Alfa AF: 0.723 Hom.: 8469

Bravo AF: 0.725

Asia WGS AF: 0.724 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.53
DANN	Benign	0.53

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: rs1874015; hg19: chr16-84877532;