16-4510928-G-C

Variant summary

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

The NM_013399.3(CDIP1):c.*1644C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,164 control chromosomes in the GnomAD database, including 41,004 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 0.73 (40994 hom., cov: 33)
  • Exomes 𝑓: 0.75 (10 hom.)
• Consequence: CDIP1 NM_013399.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

Genes affected

CDIP1 (HGNC:13234): (cell death inducing p53 target 1) Predicted to enable metal ion binding activity. Acts upstream of or within intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator and tumor necrosis factor-mediated signaling pathway. Located in cytoplasmic side of late endosome membrane; cytoplasmic side of lysosomal membrane; and nucleus. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDIP1	NM_013399.3	c.*1644C>G		3_prime_UTR_variant	6/6	ENST00000567695.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDIP1	ENST00000567695.6	c.*1644C>G		3_prime_UTR_variant	6/6	1	NM_013399.3	P1
CDIP1	ENST00000399599.7	c.*1644C>G		3_prime_UTR_variant	5/5	1		P1
CDIP1	ENST00000563332.6	c.*1644C>G		3_prime_UTR_variant	6/6	1		P1

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111242 AN: 152006 Hom.: 40940 Cov.: 33

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.724

GnomAD4 exome AF: 0.750 AC: 30 AN: 40 Hom.: 10 Cov.: 0 AF XY: 0.700 AC XY: 21 AN XY: 30

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.821

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.732 AC: 111352 AN: 152124 Hom.: 40994 Cov.: 33 AF XY: 0.727 AC XY: 54075 AN XY: 74362

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.717

Alfa AF: 0.690 Hom.: 2373

Bravo AF: 0.733

Asia WGS AF: 0.546 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.6
Dann	Benign	0.73

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: rs7702; hg19: chr16-4560929;