X-97150863-A-G

Position:

• chrX-97150863-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_006729.5(DIAPH2):​c.2719+9069A>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 0.55 (11684 hom., 17603 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: DIAPH2 NM_006729.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

Genes affected

DIAPH2 (HGNC:2877): (diaphanous related formin 2) The product of this gene belongs to the diaphanous subfamily of the formin homology family of proteins. This gene may play a role in the development and normal function of the ovaries. Defects in this gene have been linked to premature ovarian failure 2. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIAPH2	NM_006729.5	c.2719+9069A>G		intron_variant		ENST00000324765.13	NP_006720.1
DIAPH2	NM_007309.4	c.2719+9069A>G		intron_variant			NP_009293.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIAPH2	ENST00000324765.13	c.2719+9069A>G		intron_variant		1	NM_006729.5	ENSP00000321348.8
DIAPH2	ENST00000373049.8	c.2719+9069A>G		intron_variant		1		ENSP00000362140.4

Frequencies

GnomAD3 genomes AF: 0.545 AC: 60133 AN: 110311 Hom.: 11679 Cov.: 23 AF XY: 0.539 AC XY: 17574 AN XY: 32615

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.553

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.551

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: 0.545 AC: 60157 AN: 110358 Hom.: 11684 Cov.: 23 AF XY: 0.539 AC XY: 17603 AN XY: 32672

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.553

Alfa AF: 0.500 Hom.: 4568

Bravo AF: 0.542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.63

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: rs1886894; hg19: chrX-96405862;