rs58151657

chr16-84833901-G-Achr16-84833901-G-Cchr16-84833901-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.-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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRISPLD2	NM_031476.4	c.-74-4521G>A		intron_variant		ENST00000262424.10
CRISPLD2	XM_005256190.2	c.-333-2276G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.-74-4521G>A		intron_variant		1	NM_031476.4	P4
	ENST00000648152.1	n.857-5745C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.0899

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0603

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.133

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.6
Dann	Benign	0.59

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: rs58151657; hg19: chr16-84867507;