X-45196144-C-T

Position:

• chrX-45196144-C-T

Variant summary

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

The NM_176819.4(DIPK2B):​c.234-4129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 111,019 control chromosomes in the GnomAD database, including 5,466 homozygotes. There are 12,645 hemizygotes in GnomAD. 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 0.37 (5466 hom., 12645 hem., cov: 23)
• Consequence: DIPK2B NM_176819.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

Genes affected

DIPK2B (HGNC:25866): (divergent protein kinase domain 2B) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIPK2B	NM_176819.4	c.234-4129G>A		intron_variant		ENST00000398000.7	NP_789789.2
DIPK2B	NM_024689.3	c.234-4129G>A		intron_variant			NP_078965.2
DIPK2B	XM_005272670.1	c.234-4129G>A		intron_variant			XP_005272727.1
DIPK2B	XM_006724559.1	c.234-4129G>A		intron_variant			XP_006724622.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIPK2B	ENST00000398000.7	c.234-4129G>A		intron_variant		5	NM_176819.4	ENSP00000381086	P1
DIPK2B	ENST00000377934.4	c.234-4129G>A		intron_variant		1		ENSP00000367168
	ENST00000450527.5	n.94+12800C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000438181.5	n.179+12715C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.373 AC: 41379 AN: 110963 Hom.: 5469 Cov.: 23 AF XY: 0.380 AC XY: 12614 AN XY: 33219

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.476

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.373 AC: 41406 AN: 111019 Hom.: 5466 Cov.: 23 AF XY: 0.380 AC XY: 12645 AN XY: 33283

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.406

Alfa AF: 0.366 Hom.: 21538

Bravo AF: 0.384

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.16

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: rs4335267; hg19: chrX-45055389;