rs4783099

Variant names:

• chr16-84907723-C-T
• rs4783099
• NM_031476.4:c.*1081C>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.*1081C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,066 control chromosomes in the GnomAD database, including 10,585 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 0.37 (10584 hom., cov: 32)
  • Exomes 𝑓: 0.24 (1 hom.)
• Consequence: CRISPLD2 NM_031476.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 26 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 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.*1081C>T		3_prime_UTR	Exon 15 of 15	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.*1081C>T		3_prime_UTR	Exon 15 of 15	ENSP00000262424.5	Q9H0B8-1
	CRISPLD2	ENST00000941702.1		c.*1081C>T		3_prime_UTR	Exon 15 of 15	ENSP00000611761.1
	CRISPLD2	ENST00000904767.1		c.*1081C>T		3_prime_UTR	Exon 15 of 15	ENSP00000574826.1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56214 AN: 151912 Hom.: 10588 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.360

GnomAD4 exome AF: 0.235 AC: 8 AN: 34 Hom.: 1 Cov.: 0 AF XY: 0.154 AC XY: 4 AN XY: 26

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.273 AC: 6 AN: 22

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.370 AC: 56235 AN: 152032 Hom.: 10584 Cov.: 32 AF XY: 0.371 AC XY: 27585 AN XY: 74304

African (AFR) AF: 0.358 AC: 14849 AN: 41458

American (AMR) AF: 0.405 AC: 6196 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3470

East Asian (EAS) AF: 0.462 AC: 2390 AN: 5170

South Asian (SAS) AF: 0.430 AC: 2067 AN: 4802

European-Finnish (FIN) AF: 0.330 AC: 3491 AN: 10564

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24770 AN: 67970

Other (OTH) AF: 0.361 AC: 763 AN: 2112

Alfa AF: 0.366 Hom.: 15556

Bravo AF: 0.375

Asia WGS AF: 0.433 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.15
DANN	Benign	0.79
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: rs4783099; hg19: chr16-84941329;