rs3828570

Variant names:

• chr5-601532-G-A
• rs3828570
• ENST00000782781.1:n.359+9915C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-601532-G-A
• chr5-601532-G-C
• chr5-601532-G-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374608	XR_007058672.1	n.572+22G>A		intron_variant	Intron 2 of 7
LOC105374608	XR_007058673.1	n.244+22G>A		intron_variant	Intron 1 of 5
LOC105374608	XR_007058674.1	n.244+22G>A		intron_variant	Intron 1 of 6
LOC105374608	XR_007058675.1	n.244+22G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP72-DT	ENST00000782781.1	n.359+9915C>T		intron_variant	Intron 2 of 3
CEP72-DT	ENST00000782782.1	n.265+9915C>T		intron_variant	Intron 2 of 3
CEP72-DT	ENST00000782783.1	n.254-3044C>T		intron_variant	Intron 2 of 4
CEP72-DT	ENST00000782785.1	n.*27C>T		downstream_gene_variant

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 v4.3

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;