rs2304097

Positions:

• chr19-19546334-C-T

Variant summary

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

The NM_153221.2(CILP2):​c.*318C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 240,022 control chromosomes in the GnomAD database, including 1,752 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 0.091 (1581 hom., cov: 33)
  • Exomes 𝑓: 0.028 (171 hom.)
• Consequence: CILP2 NM_153221.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

Genes affected

CILP2 (HGNC:24213): (cartilage intermediate layer protein 2) Located in extracellular exosome. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CILP2	NM_153221.2	c.*318C>T		3_prime_UTR_variant	8/8	ENST00000291495.5	NP_694953.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CILP2	ENST00000291495.5	c.*318C>T		3_prime_UTR_variant	8/8	1	NM_153221.2	ENSP00000291495	P2
CILP2	ENST00000586018.5	c.*318C>T		3_prime_UTR_variant	8/8	2		ENSP00000467413	A1

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13834 AN: 152078 Hom.: 1566 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0336

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.00603

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0683

GnomAD4 exome AF: 0.0283 AC: 2488 AN: 87826 Hom.: 171 Cov.: 0 AF XY: 0.0254 AC XY: 1120 AN XY: 44030

Gnomad4 AFR exome AF: 0.255

Gnomad4 AMR exome AF: 0.0788

Gnomad4 ASJ exome AF: 0.0147

Gnomad4 EAS exome AF: 0.0446

Gnomad4 SAS exome AF: 0.109

Gnomad4 FIN exome AF: 0.00669

Gnomad4 NFE exome AF: 0.00952

Gnomad4 OTH exome AF: 0.0513

GnomAD4 genome AF: 0.0912 AC: 13880 AN: 152196 Hom.: 1581 Cov.: 33 AF XY: 0.0914 AC XY: 6805 AN XY: 74416

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.0920

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.0336

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.00603

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0312 Hom.: 312

Bravo AF: 0.103

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2304097; hg19: chr19-19657143;