rs2646112

Variant names:

• chr16-84904244-G-A
• rs2646112
• NM_031476.4:c.1440-2344G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-84904244-G-A
• chr16-84904244-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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]

ENSG00000279622 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CRISPLD2	NM_031476.4	c.1440-2344G>A		intron_variant	Intron 14 of 14	ENST00000262424.10	NP_113664.1
CRISPLD2	XM_005256190.2	c.1440-2344G>A		intron_variant	Intron 15 of 15		XP_005256247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.1440-2344G>A		intron_variant	Intron 14 of 14	1	NM_031476.4	ENSP00000262424.5
CRISPLD2	ENST00000567845.5	c.1437-2344G>A		intron_variant	Intron 14 of 14	5		ENSP00000457183.1
CRISPLD2	ENST00000566165.1	n.119+14881G>A		intron_variant	Intron 1 of 2	3		ENSP00000463171.1
ENSG00000279622	ENST00000741212.1	n.222-15878C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.442 AC: 18338 AN: 41452

American (AMR) AF: 0.149 AC: 2282 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3472

East Asian (EAS) AF: 0.466 AC: 2404 AN: 5160

South Asian (SAS) AF: 0.141 AC: 680 AN: 4826

European-Finnish (FIN) AF: 0.0541 AC: 573 AN: 10596

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0697 AC: 4743 AN: 68004

Other (OTH) AF: 0.190 AC: 402 AN: 2112

Alfa AF: 0.0938 Hom.: 810

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
PhyloP100		-0.91
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: rs2646112; hg19: chr16-84937850;