rs7912017

chr10-528952-C-Gchr10-528952-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.86-42422G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,162 control chromosomes in the GnomAD database, including 6,389 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 (6389 hom., cov: 32)
• Consequence: DIP2C NM_014974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIP2C	NM_014974.3	c.86-42422G>C		intron_variant		ENST00000280886.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIP2C	ENST00000280886.12	c.86-42422G>C		intron_variant		1	NM_014974.3	P1
DIP2C	ENST00000634311.1	c.86-42422G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37656 AN: 152044 Hom.: 6364 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.248 AC: 37717 AN: 152162 Hom.: 6389 Cov.: 32 AF XY: 0.242 AC XY: 18025 AN XY: 74392

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.222

Alfa AF: 0.214 Hom.: 602

Bravo AF: 0.259

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.88
Dann	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7912017; hg19: chr10-574892;