5-601532-G-A

Variant names:

• chr5-601532-G-A
• rs3828570
• ENST00000782781.1:n.359+9915C>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.359+9915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,066 control chromosomes in the GnomAD database, including 28,447 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 0.61 (28447 hom., cov: 32)
• Consequence: CEP72-DT ENST00000782781.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 8 publications found

Genes affected

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

LOC105374608 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP72-DT	ENST00000782781.1		n.359+9915C>T		intron	N/A
	CEP72-DT	ENST00000782782.1		n.265+9915C>T		intron	N/A
	CEP72-DT	ENST00000782783.1		n.254-3044C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92605 AN: 151948 Hom.: 28413 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.610 AC: 92692 AN: 152066 Hom.: 28447 Cov.: 32 AF XY: 0.610 AC XY: 45317 AN XY: 74332

African (AFR) AF: 0.587 AC: 24338 AN: 41458

American (AMR) AF: 0.599 AC: 9152 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1865 AN: 5172

South Asian (SAS) AF: 0.583 AC: 2809 AN: 4818

European-Finnish (FIN) AF: 0.669 AC: 7085 AN: 10584

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43408 AN: 67966

Other (OTH) AF: 0.604 AC: 1274 AN: 2110

Alfa AF: 0.577 Hom.: 6628

Bravo AF: 0.599

Asia WGS AF: 0.473 AC: 1645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.013
DANN	Benign	0.74
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs3828570; hg19: chr5-601647;