rs4881333

chr10-473224-G-Cchr10-473224-G-T

Variant summary

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

The NM_014974.3(DIP2C):c.158-675C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,144 control chromosomes in the GnomAD database, including 16,143 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 0.43 (16143 hom., cov: 33)
• Consequence: DIP2C NM_014974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIP2C	NM_014974.3	c.158-675C>G		intron_variant		ENST00000280886.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIP2C	ENST00000280886.12	c.158-675C>G		intron_variant		1	NM_014974.3	P1
DIP2C	ENST00000634311.1	c.326-675C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65551 AN: 152026 Hom.: 16146 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.431 AC: 65538 AN: 152144 Hom.: 16143 Cov.: 33 AF XY: 0.442 AC XY: 32851 AN XY: 74366

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.447

Alfa AF: 0.348 Hom.: 1038

Bravo AF: 0.416

Asia WGS AF: 0.583 AC: 2024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.015
Dann	Benign	0.26

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: rs4881333; hg19: chr10-519164;