GeneBe

chr1-222994871-T-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001377229.1(DISP1):​c.890-14T>A variant causes a intron 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

DISP1
NM_001377229.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0770

Publications

6 publications found
Variant links:
Genes affected
DISP1 (HGNC:19711): (dispatched RND transporter family member 1) The pattern of cellular proliferation and differentiation that leads to normal development of embryonic structures often depends upon the localized production of secreted protein signals. Cells surrounding the source of a particular signal respond in a graded manner according to the effective concentration of the signal, and this response produces the pattern of cell types constituting the mature structure. A novel segment-polarity gene known as dispatched has been identified in Drosophila and its protein product is required for normal Hedgehog (Hh) signaling. This gene is one of two human homologs of Drosophila dispatched and, based on sequence identity to its mouse counterpart, the encoded protein may play an essential role in Hh patterning activities in the early embryo. [provided by RefSeq, Jul 2008]
DISP1 Gene-Disease associations (from GenCC):
  • holoprosencephaly
    Inheritance: SD, AD, AR Classification: SUPPORTIVE, LIMITED Submitted by: Illumina, ClinGen, Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377229.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DISP1
NM_001377229.1
MANE Select
c.890-14T>A
intron
N/ANP_001364158.1Q96F81
DISP1
NM_001369594.1
c.890-14T>A
intron
N/ANP_001356523.1Q96F81
DISP1
NM_001377228.1
c.890-14T>A
intron
N/ANP_001364157.1Q96F81

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DISP1
ENST00000675850.1
MANE Select
c.890-14T>A
intron
N/AENSP00000502357.1Q96F81
DISP1
ENST00000284476.7
TSL:1
c.890-14T>A
intron
N/AENSP00000284476.6Q96F81
DISP1
ENST00000900747.1
c.890-14T>A
intron
N/AENSP00000570806.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1421380
Hom.:
0
Cov.:
25
AF XY:
0.00
AC XY:
0
AN XY:
709942
African (AFR)
AF:
0.00
AC:
0
AN:
32532
American (AMR)
AF:
0.00
AC:
0
AN:
44506
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25870
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39428
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85166
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52362
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5220
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1077304
Other (OTH)
AF:
0.00
AC:
0
AN:
58992
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
1265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
6.5
DANN
Benign
0.83
PhyloP100
0.077

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs2609359; hg19: chr1-223168213; API