rs2646112

chr16-84904244-G-Achr16-84904244-G-T

Variant summary

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

The NM_031476.4(CRISPLD2):c.1440-2344G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,114 control chromosomes in the GnomAD database, including 5,056 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 0.20 (5056 hom., cov: 32)
• Consequence: CRISPLD2 NM_031476.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRISPLD2	NM_031476.4	c.1440-2344G>A		intron_variant		ENST00000262424.10
CRISPLD2	XM_005256190.2	c.1440-2344G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.1440-2344G>A		intron_variant		1	NM_031476.4	P4
CRISPLD2	ENST00000567845.5	c.1437-2344G>A		intron_variant		5		A1
CRISPLD2	ENST00000566165.1	c.120+14881G>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29870 AN: 151996 Hom.: 5047 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.197 AC: 29919 AN: 152114 Hom.: 5056 Cov.: 32 AF XY: 0.196 AC XY: 14544 AN XY: 74376

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0541

Gnomad4 NFE AF: 0.0697

Gnomad4 OTH AF: 0.190

Alfa AF: 0.0909 Hom.: 688

Bravo AF: 0.218

Asia WGS AF: 0.279 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.87
Dann	Benign	0.44

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: rs2646112; hg19: chr16-84937850;