NM_001804.3:c.445+2913A>G

Variant names:

• chr5-150170234-A-G
• rs2237091
• NM_001804.3:c.445+2913A>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.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
• Publications: 6 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=-0.96).
• 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 rank	MANE	Protein	UniProt
CDX1	NM_001804.3	c.445+2913A>G		intron_variant	Intron 1 of 2	ENST00000231656.13	NP_001795.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDX1	ENST00000231656.13	c.445+2913A>G		intron_variant	Intron 1 of 2	1	NM_001804.3	ENSP00000231656.7

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

African (AFR) AF: 0.740 AC: 30674 AN: 41474

American (AMR) AF: 0.410 AC: 6263 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1996 AN: 3466

East Asian (EAS) AF: 0.553 AC: 2848 AN: 5154

South Asian (SAS) AF: 0.430 AC: 2068 AN: 4806

European-Finnish (FIN) AF: 0.351 AC: 3702 AN: 10560

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

European-Non Finnish (NFE) AF: 0.441 AC: 29964 AN: 67942

Other (OTH) AF: 0.520 AC: 1094 AN: 2104

Alfa AF: 0.473 Hom.: 4559

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
PhyloP100		0.80
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: rs2237091; hg19: chr5-149549797;