X-45172772-T-C

Variant names:

• chrX-45172772-T-C
• rs4442270
• NM_176819.4:c.499-14884A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_176819.4(DIPK2B):​c.499-14884A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.67 (17965 hom., 22239 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: DIPK2B NM_176819.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489
• Publications: 2 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIPK2B	NM_176819.4	c.499-14884A>G		intron_variant	Intron 2 of 4	ENST00000398000.7	NP_789789.2
DIPK2B	NM_024689.3	c.499-8523A>G		intron_variant	Intron 2 of 2		NP_078965.2
DIPK2B	XM_005272670.1	c.499-18574A>G		intron_variant	Intron 2 of 3		XP_005272727.1
DIPK2B	XM_006724559.1	c.499-18574A>G		intron_variant	Intron 2 of 3		XP_006724622.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIPK2B	ENST00000398000.7	c.499-14884A>G		intron_variant	Intron 2 of 4	5	NM_176819.4	ENSP00000381086.2
DIPK2B	ENST00000377934.4	c.499-8523A>G		intron_variant	Intron 2 of 2	1		ENSP00000367168.4
DIPK2B	ENST00000477281.1	n.88-18691A>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.671 AC: 74314 AN: 110759 Hom.: 17970 Cov.: 23

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.675

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.671 AC: 74357 AN: 110814 Hom.: 17965 Cov.: 23 AF XY: 0.673 AC XY: 22239 AN XY: 33030

African (AFR) AF: 0.830 AC: 25276 AN: 30463

American (AMR) AF: 0.684 AC: 7173 AN: 10481

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 1920 AN: 2626

East Asian (EAS) AF: 0.774 AC: 2694 AN: 3481

South Asian (SAS) AF: 0.737 AC: 1940 AN: 2634

European-Finnish (FIN) AF: 0.634 AC: 3702 AN: 5842

Middle Eastern (MID) AF: 0.759 AC: 164 AN: 216

European-Non Finnish (NFE) AF: 0.572 AC: 30271 AN: 52892

Other (OTH) AF: 0.677 AC: 1015 AN: 1499

Alfa AF: 0.622 Hom.: 42070

Bravo AF: 0.683

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.24
PhyloP100		0.49
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: rs4442270; hg19: chrX-45032017;