5-583327-G-A

Variant names:

• chr5-583327-G-A
• rs4957048
• ENST00000782781.1:n.360-10990C>T

Variant summary

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

The ENST00000782781.1(CEP72-DT):​n.360-10990C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,244 control chromosomes in the GnomAD database, including 2,203 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 0.16 (2203 hom., cov: 32)
• Consequence: CEP72-DT ENST00000782781.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 41 publications found

Genes affected

CEP72-DT (HGNC:55563): (CEP72 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782781.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP72-DT	ENST00000782781.1		n.360-10990C>T		intron	N/A
	CEP72-DT	ENST00000782782.1		n.266-10990C>T		intron	N/A
	CEP72-DT	ENST00000782783.1		n.383-10990C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23792 AN: 152126 Hom.: 2197 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.156 AC: 23814 AN: 152244 Hom.: 2203 Cov.: 32 AF XY: 0.156 AC XY: 11594 AN XY: 74426

African (AFR) AF: 0.0673 AC: 2796 AN: 41564

American (AMR) AF: 0.205 AC: 3138 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3470

East Asian (EAS) AF: 0.0367 AC: 190 AN: 5184

South Asian (SAS) AF: 0.195 AC: 939 AN: 4822

European-Finnish (FIN) AF: 0.144 AC: 1524 AN: 10592

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14167 AN: 68008

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.188 Hom.: 7464

Bravo AF: 0.154

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs4957048; hg19: chr5-583442;