10-555149-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.86-68619G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,834 control chromosomes in the GnomAD database, including 3,527 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 0.16 (3527 hom., cov: 32)
• Consequence: DIP2C NM_014974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530

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 (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIP2C	NM_014974.3	c.86-68619G>A		intron_variant		ENST00000280886.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIP2C	ENST00000280886.12	c.86-68619G>A		intron_variant		1	NM_014974.3	P1
DIP2C	ENST00000634311.1	c.86-68619G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.165 AC: 24982 AN: 151724 Hom.: 3516 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.0863

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.0910

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.165 AC: 25027 AN: 151834 Hom.: 3527 Cov.: 32 AF XY: 0.161 AC XY: 11931 AN XY: 74178

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.0865

Gnomad4 ASJ AF: 0.0753

Gnomad4 EAS AF: 0.0866

Gnomad4 SAS AF: 0.0807

Gnomad4 FIN AF: 0.0910

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0866 Hom.: 1274

Bravo AF: 0.172

Asia WGS AF: 0.0970 AC: 338 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	2.6
Dann	Benign	0.17

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs816650; hg19: chr10-601089;