rs6008306

chr22-46244195-G-A

Variant summary

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

The NM_207327.5(CDPF1):c.*897C>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 0.0186 in 152,222 control chromosomes in the GnomAD database, including 83 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 0.019 (83 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CDPF1 NM_207327.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

Genes affected

CDPF1 (HGNC:33710): (cysteine rich DPF motif domain containing 1)

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 = 0.0624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDPF1	NM_207327.5	c.*897C>T		3_prime_UTR_variant	4/4	ENST00000314567.8
CDPF1	XM_011529960.3	c.*619C>T		3_prime_UTR_variant	4/4
CDPF1	XM_011529965.3	c.*897C>T		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDPF1	ENST00000314567.8	c.*897C>T		3_prime_UTR_variant	4/4	1	NM_207327.5	P1
CDPF1	ENST00000381037.4	c.*1122C>T		3_prime_UTR_variant, NMD_transcript_variant	5/5	1
CDPF1	ENST00000404583.5	c.*897C>T		3_prime_UTR_variant	3/3	2
CDPF1	ENST00000404744.1	c.*1048C>T		3_prime_UTR_variant	4/4	3

Frequencies

GnomAD3 genomes AF: 0.0186 AC: 2827 AN: 152104 Hom.: 83 Cov.: 32

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00701

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000323

Gnomad OTH AF: 0.0129

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 204 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 152

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0186 AC: 2833 AN: 152222 Hom.: 83 Cov.: 32 AF XY: 0.0178 AC XY: 1326 AN XY: 74434

Gnomad4 AFR AF: 0.0645

Gnomad4 AMR AF: 0.00700

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000323

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.0110 Hom.: 5

Bravo AF: 0.0216

Asia WGS AF: 0.00318 AC: 11 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	0.57
Dann	Benign	0.67

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: rs6008306; hg19: chr22-46640092;