16-84919498-C-T

Position:

• chr16-84919498-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000625056.2(ENSG00000279622):​n.948G>A 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 0.58 in 151,602 control chromosomes in the GnomAD database, including 26,071 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 0.58 (26069 hom., cov: 30)
  • Exomes 𝑓: 0.75 (2 hom.)
• Consequence: ENSG00000279622 ENST00000625056.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

Genes affected

ENSG00000279622 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84919498C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279622	ENST00000625056.2	n.948G>A		non_coding_transcript_exon_variant	3/3	6
CRISPLD2	ENST00000566165.1	n.120-142C>T		intron_variant		3		ENSP00000463171.1

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87800 AN: 151476 Hom.: 26057 Cov.: 30

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.585

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 2 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.580 AC: 87860 AN: 151594 Hom.: 26069 Cov.: 30 AF XY: 0.585 AC XY: 43296 AN XY: 74048

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.581

Alfa AF: 0.603 Hom.: 14085

Bravo AF: 0.569

Asia WGS AF: 0.563 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2641674; hg19: chr16-84953104;