rs10795122

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000280886.12(DIP2C):​c.605-1691T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,020 control chromosomes in the GnomAD database, including 11,018 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 0.35 ( 11018 hom., cov: 32)

Consequence

DIP2C
ENST00000280886.12 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.687
Variant links:
Genes affected
DIP2C (HGNC:29150): (disco interacting protein 2 homolog C) This gene encodes a member of the disco-interacting protein homolog 2 family. The protein shares strong similarity with a Drosophila protein which interacts with the transcription factor disco and is expressed in the nervous system. [provided by RefSeq, Oct 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DIP2CNM_014974.3 linkuse as main transcriptc.605-1691T>C intron_variant ENST00000280886.12 NP_055789.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DIP2CENST00000280886.12 linkuse as main transcriptc.605-1691T>C intron_variant 1 NM_014974.3 ENSP00000280886 P1Q9Y2E4-1
DIP2CENST00000634311.1 linkuse as main transcriptc.773-1691T>C intron_variant 5 ENSP00000489203

Frequencies

GnomAD3 genomes
AF:
0.355
AC:
53885
AN:
151902
Hom.:
11007
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.141
Gnomad AMI
AF:
0.575
Gnomad AMR
AF:
0.380
Gnomad ASJ
AF:
0.383
Gnomad EAS
AF:
0.322
Gnomad SAS
AF:
0.330
Gnomad FIN
AF:
0.411
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.470
Gnomad OTH
AF:
0.372
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.355
AC:
53908
AN:
152020
Hom.:
11018
Cov.:
32
AF XY:
0.351
AC XY:
26047
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.141
Gnomad4 AMR
AF:
0.380
Gnomad4 ASJ
AF:
0.383
Gnomad4 EAS
AF:
0.322
Gnomad4 SAS
AF:
0.332
Gnomad4 FIN
AF:
0.411
Gnomad4 NFE
AF:
0.470
Gnomad4 OTH
AF:
0.374
Alfa
AF:
0.397
Hom.:
1772
Bravo
AF:
0.341
Asia WGS
AF:
0.342
AC:
1188
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.46
DANN
Benign
0.38

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10795122; hg19: chr10-466830; API