5-150176995-T-G

Variant names:

• chr5-150176995-T-G
• rs717746
• NM_001804.3:c.446-5773T>G

Variant summary

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

The NM_001804.3(CDX1):​c.446-5773T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,152 control chromosomes in the GnomAD database, including 22,371 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 (22371 hom., cov: 34)
• Consequence: CDX1 NM_001804.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 8 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001804.3. 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
	CDX1	NM_001804.3	MANE Select	c.446-5773T>G		intron	N/A	NP_001795.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDX1	ENST00000231656.13	TSL:1 MANE Select	c.446-5773T>G		intron	N/A	ENSP00000231656.7

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79477 AN: 152034 Hom.: 22331 Cov.: 34

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.523 AC: 79574 AN: 152152 Hom.: 22371 Cov.: 34 AF XY: 0.516 AC XY: 38379 AN XY: 74376

African (AFR) AF: 0.739 AC: 30691 AN: 41530

American (AMR) AF: 0.411 AC: 6293 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2071 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2910 AN: 5162

South Asian (SAS) AF: 0.435 AC: 2099 AN: 4820

European-Finnish (FIN) AF: 0.351 AC: 3718 AN: 10584

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 30006 AN: 67976

Other (OTH) AF: 0.523 AC: 1105 AN: 2112

Alfa AF: 0.463 Hom.: 28095

Bravo AF: 0.536

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.87
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs717746; hg19: chr5-149556558;