ENST00000424691.3:n.904-670G>A

Variant names:

• chr3-10018741-C-T
• rs6804473
• ENST00000424691.3:n.904-670G>A

Variant summary

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

The ENST00000424691.3(ENSG00000291078):​n.904-670G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,580 control chromosomes in the GnomAD database, including 5,292 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 0.22 (5292 hom., cov: 32)
• Consequence: ENSG00000291078 ENST00000424691.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 8 publications found

Genes affected

ENSG00000291078 (HGNC:):

CIDECP1 (HGNC:24230): (CIDEC pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424691.3. 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
	CIDECP1	NR_002786.1		n.285-670G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291078	ENST00000424691.3	TSL:1	n.904-670G>A		intron	N/A
	ENSG00000291078	ENST00000432401.8	TSL:1	n.528-3215G>A		intron	N/A
	ENSG00000291078	ENST00000335507.12	TSL:3	n.921-3215G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33973 AN: 151464 Hom.: 5284 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.224 AC: 34009 AN: 151580 Hom.: 5292 Cov.: 32 AF XY: 0.218 AC XY: 16131 AN XY: 74064

African (AFR) AF: 0.417 AC: 17139 AN: 41072

American (AMR) AF: 0.154 AC: 2345 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3468

East Asian (EAS) AF: 0.0664 AC: 343 AN: 5166

South Asian (SAS) AF: 0.172 AC: 811 AN: 4724

European-Finnish (FIN) AF: 0.110 AC: 1173 AN: 10616

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10979 AN: 67994

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.155 Hom.: 1129

Bravo AF: 0.240

Asia WGS AF: 0.126 AC: 439 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6804473; hg19: chr3-10060425;