rs3812863

Variant names:

• chr13-27971131-G-A
• rs3812863
• ENST00000947371.1:c.-57-2068C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-27971131-G-A
• chr13-27971131-G-C

Variant summary

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

The ENST00000947371.1(CDX2):​c.-57-2068C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,040 control chromosomes in the GnomAD database, including 18,853 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 0.48 (18844 hom., cov: 32)
  • Exomes 𝑓: 0.74 (9 hom.)
• Consequence: CDX2 ENST00000947371.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 12 publications found

Genes affected

CDX2 (HGNC:1806): (caudal type homeobox 2) This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded protein is a major regulator of intestine-specific genes involved in cell growth an differentiation. This protein also plays a role in early embryonic development of the intestinal tract. Aberrant expression of this gene is associated with intestinal inflammation and tumorigenesis. [provided by RefSeq, Jan 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000947371.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDX2	ENST00000947371.1		c.-57-2068C>T		intron	N/A	ENSP00000617430.1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72847 AN: 151882 Hom.: 18840 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.503

GnomAD4 exome AF: 0.737 AC: 28 AN: 38 Hom.: 9 Cov.: 0 AF XY: 0.773 AC XY: 17 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.765 AC: 26 AN: 34

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.479 AC: 72873 AN: 152002 Hom.: 18844 Cov.: 32 AF XY: 0.482 AC XY: 35804 AN XY: 74258

African (AFR) AF: 0.300 AC: 12438 AN: 41480

American (AMR) AF: 0.390 AC: 5955 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1985 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2234 AN: 5146

South Asian (SAS) AF: 0.721 AC: 3468 AN: 4812

European-Finnish (FIN) AF: 0.580 AC: 6115 AN: 10542

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39100 AN: 67958

Other (OTH) AF: 0.504 AC: 1064 AN: 2110

Alfa AF: 0.539 Hom.: 38134

Bravo AF: 0.447

Asia WGS AF: 0.577 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.94
PhyloP100		0.049
Mutation Taster		=300/0	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: rs3812863; hg19: chr13-28545268;