16-84843926-T-C

Variant names:

• chr16-84843926-T-C
• rs1874015
• NM_031476.4:c.241-1860T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ENSG00000285848 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CRISPLD2	NM_031476.4	c.241-1860T>C		intron_variant	Intron 2 of 14	ENST00000262424.10	NP_113664.1
CRISPLD2	XM_005256190.2	c.241-1860T>C		intron_variant	Intron 3 of 15		XP_005256247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.241-1860T>C		intron_variant	Intron 2 of 14	1	NM_031476.4	ENSP00000262424.5

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

African (AFR) AF: 0.765 AC: 31746 AN: 41494

American (AMR) AF: 0.757 AC: 11571 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2425 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3062 AN: 5148

South Asian (SAS) AF: 0.753 AC: 3629 AN: 4822

European-Finnish (FIN) AF: 0.730 AC: 7731 AN: 10596

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48122 AN: 67996

Other (OTH) AF: 0.713 AC: 1507 AN: 2114

Alfa AF: 0.725 Hom.: 8708

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
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1874015; hg19: chr16-84877532;