16-84919498-C-T

Variant names:

• chr16-84919498-C-T
• rs2641674
• ENST00000625056.2:n.948G>A

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279622	ENST00000625056.2	n.948G>A		non_coding_transcript_exon_variant	Exon 3 of 3	6
CRISPLD2	ENST00000566165.1	n.120-142C>T		intron_variant	Intron 1 of 2	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;