10-388696-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.1598-887G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,082 control chromosomes in the GnomAD database, including 22,049 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 0.54 (22049 hom., cov: 33)
• Consequence: DIP2C NM_014974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.81

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 = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIP2C	NM_014974.3	c.1598-887G>A		intron_variant		ENST00000280886.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIP2C	ENST00000280886.12	c.1598-887G>A		intron_variant		1	NM_014974.3	P1
DIP2C	ENST00000421992.2	c.27-887G>A		intron_variant		5
DIP2C	ENST00000634311.1	c.1766-887G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81451 AN: 151964 Hom.: 22045 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.536 AC: 81481 AN: 152082 Hom.: 22049 Cov.: 33 AF XY: 0.545 AC XY: 40490 AN XY: 74334

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.525

Alfa AF: 0.535 Hom.: 4315

Bravo AF: 0.530

Asia WGS AF: 0.678 AC: 2357 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	0.043
Dann	Benign	0.59

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: rs7914284; hg19: chr10-434636;