X-97151055-C-T

Position:

• chrX-97151055-C-T

Variant summary

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

The NM_006729.5(DIAPH2):​c.2719+9261C>T 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 (11789 hom., 17725 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: DIAPH2 NM_006729.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

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=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIAPH2	NM_006729.5	c.2719+9261C>T		intron_variant		ENST00000324765.13
DIAPH2	NM_007309.4	c.2719+9261C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIAPH2	ENST00000324765.13	c.2719+9261C>T		intron_variant		1	NM_006729.5	A2
DIAPH2	ENST00000373049.8	c.2719+9261C>T		intron_variant		1		P3

Frequencies

GnomAD3 genomes AF: 0.549 AC: 60480 AN: 110096 Hom.: 11784 Cov.: 22 AF XY: 0.546 AC XY: 17698 AN XY: 32410

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.549

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.554

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: 0.549 AC: 60500 AN: 110148 Hom.: 11789 Cov.: 22 AF XY: 0.546 AC XY: 17725 AN XY: 32472

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.556

Alfa AF: 0.569 Hom.: 4248

Bravo AF: 0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.19

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: rs1012930; hg19: chrX-96406054;