rs10904051

Positions:

• chr10-362368-A-G

Variant summary

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

The NM_014974.3(DIP2C):​c.2794+122T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,154,162 control chromosomes in the GnomAD database, including 142,570 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 0.40 (13939 hom., cov: 32)
  • Exomes 𝑓: 0.50 (128631 hom.)
• Consequence: DIP2C NM_014974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.726

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=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIP2C	NM_014974.3	c.2794+122T>C		intron_variant		ENST00000280886.12	NP_055789.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIP2C	ENST00000280886.12	c.2794+122T>C		intron_variant		1	NM_014974.3	ENSP00000280886.6
DIP2C	ENST00000634311.1	c.2962+122T>C		intron_variant		5		ENSP00000489203.1

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60422 AN: 151914 Hom.: 13934 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.427

GnomAD4 exome AF: 0.497 AC: 498333 AN: 1002130 Hom.: 128631 AF XY: 0.494 AC XY: 244229 AN XY: 494004

Gnomad4 AFR exome AF: 0.130

Gnomad4 AMR exome AF: 0.404

Gnomad4 ASJ exome AF: 0.472

Gnomad4 EAS exome AF: 0.258

Gnomad4 SAS exome AF: 0.374

Gnomad4 FIN exome AF: 0.453

Gnomad4 NFE exome AF: 0.534

Gnomad4 OTH exome AF: 0.468

GnomAD4 genome AF: 0.398 AC: 60437 AN: 152032 Hom.: 13939 Cov.: 32 AF XY: 0.392 AC XY: 29121 AN XY: 74292

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.426

Alfa AF: 0.488 Hom.: 4644

Bravo AF: 0.383

Asia WGS AF: 0.337 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.3
DANN	Benign	0.86

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: rs10904051; hg19: chr10-408308;