X-45196144-C-T

Variant names:

• chrX-45196144-C-T
• rs4335267
• NM_176819.4:c.234-4129G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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]

ENSG00000229491 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DIPK2B	NM_176819.4	c.234-4129G>A		intron_variant	Intron 1 of 4	ENST00000398000.7	NP_789789.2
DIPK2B	NM_024689.3	c.234-4129G>A		intron_variant	Intron 1 of 2		NP_078965.2
DIPK2B	XM_005272670.1	c.234-4129G>A		intron_variant	Intron 1 of 3		XP_005272727.1
DIPK2B	XM_006724559.1	c.234-4129G>A		intron_variant	Intron 1 of 3		XP_006724622.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIPK2B	ENST00000398000.7	c.234-4129G>A		intron_variant	Intron 1 of 4	5	NM_176819.4	ENSP00000381086.2
DIPK2B	ENST00000377934.4	c.234-4129G>A		intron_variant	Intron 1 of 2	1		ENSP00000367168.4
ENSG00000229491	ENST00000438181.5	n.179+12715C>T		intron_variant	Intron 1 of 3	3
ENSG00000229491	ENST00000450527.5	n.94+12800C>T		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.373 AC: 41379 AN: 110963 Hom.: 5469 Cov.: 23

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

African (AFR) AF: 0.359 AC: 10988 AN: 30566

American (AMR) AF: 0.506 AC: 5281 AN: 10446

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1083 AN: 2635

East Asian (EAS) AF: 0.307 AC: 1074 AN: 3495

South Asian (SAS) AF: 0.496 AC: 1331 AN: 2684

European-Finnish (FIN) AF: 0.425 AC: 2492 AN: 5869

Middle Eastern (MID) AF: 0.502 AC: 106 AN: 211

European-Non Finnish (NFE) AF: 0.345 AC: 18253 AN: 52929

Other (OTH) AF: 0.406 AC: 609 AN: 1501

Alfa AF: 0.374 Hom.: 33234

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
PhyloP100		-0.43
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: rs4335267; hg19: chrX-45055389;