16-84838445-G-C

Variant names:

• chr16-84838445-G-C
• rs1546124
• ENST00000565561.1:n.161G>C

Variant summary

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

The ENST00000565561.1(CRISPLD2):​n.161G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 1,584,088 control chromosomes in the GnomAD database, including 366,443 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 0.69 (36984 hom., cov: 33)
  • Exomes 𝑓: 0.68 (329459 hom.)
• Consequence: CRISPLD2 ENST00000565561.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 28 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRISPLD2	NM_031476.4	c.-51G>C		5_prime_UTR_variant	Exon 2 of 15	ENST00000262424.10	NP_113664.1
CRISPLD2	XM_005256190.2	c.-51G>C		5_prime_UTR_variant	Exon 3 of 16		XP_005256247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRISPLD2	ENST00000262424.10	c.-51G>C		5_prime_UTR_variant	Exon 2 of 15	1	NM_031476.4	ENSP00000262424.5

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105462 AN: 151960 Hom.: 36953 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.677

GnomAD2 exomes AF: 0.668 AC: 155429 AN: 232544 AF XY: 0.668

Gnomad AFR exome AF: 0.750

Gnomad AMR exome AF: 0.683

Gnomad ASJ exome AF: 0.658

Gnomad EAS exome AF: 0.412

Gnomad FIN exome AF: 0.734

Gnomad NFE exome AF: 0.680

Gnomad OTH exome AF: 0.663

GnomAD4 exome AF: 0.676 AC: 968609 AN: 1432010 Hom.: 329459 Cov.: 39 AF XY: 0.676 AC XY: 478859 AN XY: 708480

African (AFR) AF: 0.751 AC: 24767 AN: 32970

American (AMR) AF: 0.685 AC: 29568 AN: 43178

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 15980 AN: 24132

East Asian (EAS) AF: 0.463 AC: 18204 AN: 39320

South Asian (SAS) AF: 0.690 AC: 56349 AN: 81678

European-Finnish (FIN) AF: 0.731 AC: 37742 AN: 51604

Middle Eastern (MID) AF: 0.616 AC: 3079 AN: 5000

European-Non Finnish (NFE) AF: 0.679 AC: 743771 AN: 1095024

Other (OTH) AF: 0.662 AC: 39149 AN: 59104

GnomAD4 genome AF: 0.694 AC: 105550 AN: 152078 Hom.: 36984 Cov.: 33 AF XY: 0.695 AC XY: 51637 AN XY: 74344

African (AFR) AF: 0.751 AC: 31145 AN: 41486

American (AMR) AF: 0.681 AC: 10391 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2322 AN: 3468

East Asian (EAS) AF: 0.434 AC: 2238 AN: 5156

South Asian (SAS) AF: 0.687 AC: 3317 AN: 4828

European-Finnish (FIN) AF: 0.739 AC: 7820 AN: 10578

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46166 AN: 67980

Other (OTH) AF: 0.680 AC: 1434 AN: 2110

Alfa AF: 0.633 Hom.: 3285

Bravo AF: 0.687

Asia WGS AF: 0.602 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.44
PhyloP100		-1.4
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1546124; hg19: chr16-84872051; COSMIC: COSV52278536; COSMIC: COSV52278536;