10-520439-C-T

Position:

• chr10-520439-C-T

Variant summary

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

The NM_014974.3(DIP2C):​c.86-33909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,166 control chromosomes in the GnomAD database, including 5,877 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 0.25 (5877 hom., cov: 34)
• Consequence: DIP2C NM_014974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIP2C	NM_014974.3	c.86-33909G>A		intron_variant		ENST00000280886.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIP2C	ENST00000280886.12	c.86-33909G>A		intron_variant		1	NM_014974.3	P1
DIP2C	ENST00000634311.1	c.86-33909G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37814 AN: 152048 Hom.: 5872 Cov.: 34

Gnomad AFR AF: 0.0700

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.249 AC: 37827 AN: 152166 Hom.: 5877 Cov.: 34 AF XY: 0.247 AC XY: 18359 AN XY: 74394

Gnomad4 AFR AF: 0.0698

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.0692

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.277

Alfa AF: 0.309 Hom.: 7019

Bravo AF: 0.237

Asia WGS AF: 0.182 AC: 634 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	1.2
DANN	Benign	0.30

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: rs11252926; hg19: chr10-566379;