rs10795122

Positions:

• chr10-420890-A-G
• chr10-420890-A-T

Variant summary

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

The NM_014974.3(DIP2C):​c.605-1691T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,020 control chromosomes in the GnomAD database, including 11,018 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 0.35 (11018 hom., cov: 32)
• Consequence: DIP2C NM_014974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

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 = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIP2C	NM_014974.3	c.605-1691T>C		intron_variant		ENST00000280886.12	NP_055789.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIP2C	ENST00000280886.12	c.605-1691T>C		intron_variant		1	NM_014974.3	ENSP00000280886.6
DIP2C	ENST00000634311.1	c.773-1691T>C		intron_variant		5		ENSP00000489203.1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53885 AN: 151902 Hom.: 11007 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.355 AC: 53908 AN: 152020 Hom.: 11018 Cov.: 32 AF XY: 0.351 AC XY: 26047 AN XY: 74290

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.374

Alfa AF: 0.397 Hom.: 1772

Bravo AF: 0.341

Asia WGS AF: 0.342 AC: 1188 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	0.46
DANN	Benign	0.38

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: rs10795122; hg19: chr10-466830;