rs10489191

chr1-167536658-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000466652.2(CREG1):c.660-3261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,222 control chromosomes in the GnomAD database, including 446 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 0.068 (446 hom., cov: 32)
• Consequence: CREG1 ENST00000466652.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

CREG1 (HGNC:2351): (cellular repressor of E1A stimulated genes 1) The adenovirus E1A protein both activates and represses gene expression to promote cellular proliferation and inhibit differentiation. The protein encoded by this gene antagonizes transcriptional activation and cellular transformation by E1A. This protein shares limited sequence similarity with E1A and binds both the general transcription factor TBP and the tumor suppressor pRb in vitro. This gene may contribute to the transcriptional control of cell growth and differentiation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CREG1	ENST00000466652.2	c.660-3261A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10309 AN: 152104 Hom.: 446 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0692

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0238

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.0758

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

GnomAD4 genome AF: 0.0677 AC: 10303 AN: 152222 Hom.: 446 Cov.: 32 AF XY: 0.0667 AC XY: 4963 AN XY: 74418

Gnomad4 AFR AF: 0.0168

Gnomad4 AMR AF: 0.0690

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0239

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0404

Gnomad4 NFE AF: 0.0987

Gnomad4 OTH AF: 0.0745

Alfa AF: 0.0969 Hom.: 380

Bravo AF: 0.0661

Asia WGS AF: 0.0710 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.79
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489191; hg19: chr1-167505895;