NM_176819.4:c.498+16876T>G

Variant names:

• chrX-45174875-A-C
• rs4610880
• NM_176819.4:c.498+16876T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_176819.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIPK2B	NM_176819.4	MANE Select	c.498+16876T>G		intron	N/A	NP_789789.2
	DIPK2B	NM_024689.3		c.499-10626T>G		intron	N/A	NP_078965.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIPK2B	ENST00000398000.7	TSL:5 MANE Select	c.498+16876T>G		intron	N/A	ENSP00000381086.2
	DIPK2B	ENST00000377934.4	TSL:1	c.499-10626T>G		intron	N/A	ENSP00000367168.4
	DIPK2B	ENST00000477281.1	TSL:5	n.87+16972T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 26391 AN: 111083 Hom.: 2818 Cov.: 22

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

African (AFR) AF: 0.428 AC: 13002 AN: 30409

American (AMR) AF: 0.157 AC: 1652 AN: 10536

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 511 AN: 2643

East Asian (EAS) AF: 0.0450 AC: 160 AN: 3559

South Asian (SAS) AF: 0.190 AC: 508 AN: 2674

European-Finnish (FIN) AF: 0.206 AC: 1217 AN: 5899

Middle Eastern (MID) AF: 0.262 AC: 56 AN: 214

European-Non Finnish (NFE) AF: 0.167 AC: 8829 AN: 53009

Other (OTH) AF: 0.212 AC: 321 AN: 1516

Alfa AF: 0.198 Hom.: 6133

Bravo AF: 0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.73
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4610880; hg19: chrX-45034120;