ENST00000625056.3:n.1037G>A

Variant names:

• chr16-84919498-C-T
• rs2641674
• ENST00000625056.3:n.1037G>A

Variant summary

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

The ENST00000625056.3(ENSG00000279622):​n.1037G>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 ENST00000625056.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000625056.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279622	ENST00000625056.3	TSL:6	n.1037G>A		non_coding_transcript_exon	Exon 3 of 3
	CRISPLD2	ENST00000566165.1	TSL:3	n.120-142C>T		intron	N/A	ENSP00000463171.1
	ENSG00000279622	ENST00000741212.1		n.221+4045G>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 6 AN: 8

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.429 AC: 17712 AN: 41246

American (AMR) AF: 0.674 AC: 10275 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2020 AN: 3466

East Asian (EAS) AF: 0.550 AC: 2822 AN: 5132

South Asian (SAS) AF: 0.603 AC: 2889 AN: 4792

European-Finnish (FIN) AF: 0.660 AC: 6891 AN: 10448

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43328 AN: 67954

Other (OTH) AF: 0.581 AC: 1224 AN: 2106

Alfa AF: 0.607 Hom.: 19767

Bravo AF: 0.569

Asia WGS AF: 0.563 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.49
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs2641674; hg19: chr16-84953104;