rs17293454

chr10-587555-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014974.3(DIP2C):c.86-101025A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 152,162 control chromosomes in the GnomAD database, including 652 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 0.077 (652 hom., cov: 32)
• Consequence: DIP2C NM_014974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIP2C	NM_014974.3	c.86-101025A>G		intron_variant		ENST00000280886.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIP2C	ENST00000280886.12	c.86-101025A>G		intron_variant		1	NM_014974.3	P1
DIP2C	ENST00000634311.1	c.86-101025A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11727 AN: 152042 Hom.: 652 Cov.: 32

Gnomad AFR AF: 0.0197

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0417

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0718

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0771 AC: 11726 AN: 152162 Hom.: 652 Cov.: 32 AF XY: 0.0771 AC XY: 5734 AN XY: 74376

Gnomad4 AFR AF: 0.0196

Gnomad4 AMR AF: 0.0417

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0566

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0706

Alfa AF: 0.109 Hom.: 449

Bravo AF: 0.0672

Asia WGS AF: 0.0240 AC: 83 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	3.1
Dann	Benign	0.50
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		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

LitVar

Other links and lift over

dbSNP: rs17293454; hg19: chr10-633495;