chr16-84833901-G-A

Variant names:

• chr16-84833901-G-A
• rs58151657
• NM_031476.4:c.-74-4521G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031476.4(CRISPLD2):​c.-74-4521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,224 control chromosomes in the GnomAD database, including 1,476 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 0.13 (1476 hom., cov: 33)
• Consequence: CRISPLD2 NM_031476.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 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.-74-4521G>A		intron	N/A	NP_113664.1	Q9H0B8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD2	ENST00000262424.10	TSL:1 MANE Select	c.-74-4521G>A		intron	N/A	ENSP00000262424.5	Q9H0B8-1
	CRISPLD2	ENST00000564567.5	TSL:1	c.-74-4521G>A		intron	N/A	ENSP00000457655.1	Q9H0B8-2
	CRISPLD2	ENST00000569090.1	TSL:1	c.-74-4521G>A		intron	N/A	ENSP00000454858.1	Q9H0B8-5

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19856 AN: 152106 Hom.: 1457 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0901

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.131 AC: 19926 AN: 152224 Hom.: 1476 Cov.: 33 AF XY: 0.129 AC XY: 9610 AN XY: 74430

African (AFR) AF: 0.197 AC: 8182 AN: 41500

American (AMR) AF: 0.0899 AC: 1375 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3472

East Asian (EAS) AF: 0.0603 AC: 312 AN: 5174

South Asian (SAS) AF: 0.130 AC: 627 AN: 4826

European-Finnish (FIN) AF: 0.0923 AC: 980 AN: 10620

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7342 AN: 68016

Other (OTH) AF: 0.133 AC: 280 AN: 2110

Alfa AF: 0.0501 Hom.: 62

Bravo AF: 0.134

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.59
PhyloP100		1.2
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: rs58151657; hg19: chr16-84867507;