16-84853638-C-T

Variant names:

• chr16-84853638-C-T
• rs2646129
• NM_031476.4:c.609-1091C>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.609-1091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,062 control chromosomes in the GnomAD database, including 31,779 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 0.64 (31779 hom., cov: 32)
• Consequence: CRISPLD2 NM_031476.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031476.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD2	NM_031476.4	MANE Select	c.609-1091C>T		intron	N/A	NP_113664.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD2	ENST00000262424.10	TSL:1 MANE Select	c.609-1091C>T		intron	N/A	ENSP00000262424.5
	CRISPLD2	ENST00000564567.5	TSL:1	c.609-1091C>T		intron	N/A	ENSP00000457655.1
	CRISPLD2	ENST00000941702.1		c.609-1091C>T		intron	N/A	ENSP00000611761.1

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97215 AN: 151944 Hom.: 31760 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.640 AC: 97273 AN: 152062 Hom.: 31779 Cov.: 32 AF XY: 0.643 AC XY: 47827 AN XY: 74334

African (AFR) AF: 0.509 AC: 21085 AN: 41464

American (AMR) AF: 0.751 AC: 11474 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2539 AN: 3472

East Asian (EAS) AF: 0.822 AC: 4239 AN: 5156

South Asian (SAS) AF: 0.729 AC: 3515 AN: 4822

European-Finnish (FIN) AF: 0.620 AC: 6565 AN: 10586

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45537 AN: 67958

Other (OTH) AF: 0.658 AC: 1390 AN: 2114

Alfa AF: 0.668 Hom.: 18569

Bravo AF: 0.644

Asia WGS AF: 0.717 AC: 2494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0030
DANN	Benign	0.54
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: rs2646129; hg19: chr16-84887244;