16-84911573-G-T

Variant names:

• chr16-84911573-G-T
• rs903194
• ENST00000741215.1:n.62C>A

Variant summary

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

The ENST00000741215.1(ENSG00000279622):​n.62C>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 0.667 in 151,942 control chromosomes in the GnomAD database, including 33,979 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 0.67 (33979 hom., cov: 31)
• Consequence: ENSG00000279622 ENST00000741215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.706 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	ENST00000741215.1	n.62C>A		non_coding_transcript_exon_variant	Exon 1 of 2
CRISPLD2	ENST00000566165.1	n.120-8067G>T		intron_variant	Intron 1 of 2	3		ENSP00000463171.1
ENSG00000279622	ENST00000741212.1	n.221+11970C>A		intron_variant	Intron 2 of 2
ENSG00000279622	ENST00000741213.1	n.206-591C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101284 AN: 151826 Hom.: 33953 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.671

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.667 AC: 101361 AN: 151942 Hom.: 33979 Cov.: 31 AF XY: 0.672 AC XY: 49936 AN XY: 74258

African (AFR) AF: 0.712 AC: 29478 AN: 41416

American (AMR) AF: 0.717 AC: 10959 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2801 AN: 5158

South Asian (SAS) AF: 0.613 AC: 2948 AN: 4810

European-Finnish (FIN) AF: 0.706 AC: 7454 AN: 10562

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.638 AC: 43344 AN: 67944

Other (OTH) AF: 0.672 AC: 1413 AN: 2104

Alfa AF: 0.644 Hom.: 49547

Bravo AF: 0.666

Asia WGS AF: 0.611 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.72
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs903194; hg19: chr16-84945179;