rs1974047

Variant names:

• chr13-19130775-A-G
• rs1974047

Variant summary

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

The variant allele was found at a frequency of 0.681 in 151,872 control chromosomes in the GnomAD database, including 35,607 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 0.68 (35607 hom., cov: 30)
• Consequence: CENPIP1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 2 publications found

Genes affected

CENPIP1 (HGNC:39575): (centromere protein I pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425713.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CENPIP1	ENST00000425713.1	TSL:6	n.493-517A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103395 AN: 151754 Hom.: 35580 Cov.: 30

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.681 AC: 103460 AN: 151872 Hom.: 35607 Cov.: 30 AF XY: 0.676 AC XY: 50144 AN XY: 74194

African (AFR) AF: 0.614 AC: 25389 AN: 41380

American (AMR) AF: 0.639 AC: 9747 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2409 AN: 3472

East Asian (EAS) AF: 0.474 AC: 2428 AN: 5126

South Asian (SAS) AF: 0.618 AC: 2980 AN: 4822

European-Finnish (FIN) AF: 0.719 AC: 7578 AN: 10542

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.744 AC: 50592 AN: 67968

Other (OTH) AF: 0.667 AC: 1409 AN: 2112

Alfa AF: 0.709 Hom.: 14134

Bravo AF: 0.669

Asia WGS AF: 0.529 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.83
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs1974047; hg19: chr13-19704915;