rs2237091

chr5-150170234-A-G

Variant summary

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

The NM_001804.3(CDX1):c.445+2913A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,998 control chromosomes in the GnomAD database, including 22,250 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 0.52 (22250 hom., cov: 32)
• Consequence: CDX1 NM_001804.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801

Genes affected

CDX1 (HGNC:1805): (caudal type homeobox 1) This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded DNA-binding protein regulates intestine-specific gene expression and enterocyte differentiation. It has been shown to induce expression of the intestinal alkaline phosphatase gene, and inhibit beta-catenin/T-cell factor transcriptional activity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDX1	NM_001804.3	c.445+2913A>G		intron_variant		ENST00000231656.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDX1	ENST00000231656.13	c.445+2913A>G		intron_variant		1	NM_001804.3	P1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79202 AN: 151880 Hom.: 22209 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.522 AC: 79299 AN: 151998 Hom.: 22250 Cov.: 32 AF XY: 0.514 AC XY: 38211 AN XY: 74284

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.520

Alfa AF: 0.468 Hom.: 4353

Bravo AF: 0.534

Asia WGS AF: 0.512 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.0
Dann	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2237091; hg19: chr5-149549797;