rs10489191

Variant names:

• chr1-167536658-T-C
• rs10489191
• ENST00000466652.2:c.660-3261A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000466652.2. 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
	CREG1	ENST00000466652.2	TSL:3	c.660-3261A>G		intron	N/A	ENSP00000496871.1

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

African (AFR) AF: 0.0168 AC: 700 AN: 41552

American (AMR) AF: 0.0690 AC: 1055 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3470

East Asian (EAS) AF: 0.0239 AC: 123 AN: 5152

South Asian (SAS) AF: 0.116 AC: 560 AN: 4828

European-Finnish (FIN) AF: 0.0404 AC: 429 AN: 10616

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0987 AC: 6712 AN: 68008

Other (OTH) AF: 0.0745 AC: 157 AN: 2106

Alfa AF: 0.0966 Hom.: 407

Bravo AF: 0.0661

Asia WGS AF: 0.0710 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.79
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10489191; hg19: chr1-167505895;