dbSNP rs2209172: DMBX1:c.*331C>A (chr1-46512825-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_172225.2(DMBX1):c.*331C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

DMBX1
NM_172225.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.996

Publications

0 publications found

Variant links:

Genes affected

DMBX1 (HGNC:19026): (diencephalon/mesencephalon homeobox 1) This gene encodes a member of the bicoid sub-family of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and may play a role in brain and sensory organ development. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

DMBX1 Gene-Disease associations (from GenCC):

complex neurodevelopmental disorder
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

DMBX1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
DMBX1	NM_172225.2 link	c.*331C>A	3_prime_UTR_variant	Exon 6 of 6	ENST00000360032.4	NP_757379.1	Q8NFW5-2
DMBX1	NM_001387776.1 link	c.*331C>A	3_prime_UTR_variant	Exon 5 of 5		NP_001374705.1
DMBX1	NM_147192.4 link	c.*331C>A	3_prime_UTR_variant	Exon 6 of 6		NP_671725.1	Q8NFW5-1
DMBX1	NM_001387775.1 link	c.*331C>A	3_prime_UTR_variant	Exon 5 of 5		NP_001374704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMBX1	ENST00000360032.4 link	c.*331C>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_172225.2	ENSP00000353132.3		Q8NFW5-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

174036

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

88046

African (AFR)

AF:

0.00

AC:

AN:

6568

American (AMR)

AF:

0.00

AC:

AN:

7516

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6436

East Asian (EAS)

AF:

0.00

AC:

AN:

14408

South Asian (SAS)

AF:

0.00

AC:

AN:

5988

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10854

Middle Eastern (MID)

AF:

0.00

AC:

AN:

886

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

109854

Other (OTH)

AF:

0.00

AC:

AN:

11526

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

8.2

(source)

DANN

Benign

0.80

PhyloP100

1.0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over