X-45174875-A-C

Position:

• chrX-45174875-A-C

Variant summary

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

The NM_176819.4(DIPK2B):​c.498+16876T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 111,134 control chromosomes in the GnomAD database, including 2,822 homozygotes. There are 7,583 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 0.24 (2822 hom., 7583 hem., cov: 22)
• Consequence: DIPK2B NM_176819.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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]

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 = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIPK2B	NM_176819.4	c.498+16876T>G		intron_variant		ENST00000398000.7
DIPK2B	NM_024689.3	c.499-10626T>G		intron_variant
DIPK2B	XM_005272670.1	c.498+16876T>G		intron_variant
DIPK2B	XM_006724559.1	c.498+16876T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIPK2B	ENST00000398000.7	c.498+16876T>G		intron_variant		5	NM_176819.4	P1
DIPK2B	ENST00000377934.4	c.499-10626T>G		intron_variant		1
DIPK2B	ENST00000477281.1	n.87+16972T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.238 AC: 26391 AN: 111083 Hom.: 2818 Cov.: 22 AF XY: 0.227 AC XY: 7565 AN XY: 33309

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.238

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.238 AC: 26411 AN: 111134 Hom.: 2822 Cov.: 22 AF XY: 0.227 AC XY: 7583 AN XY: 33370

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0450

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.212

Alfa AF: 0.188 Hom.: 3836

Bravo AF: 0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.73

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: rs4610880; hg19: chrX-45034120;