rs233214

chrX-96887520-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006729.5(DIAPH2):c.587+5802C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 109,628 control chromosomes in the GnomAD database, including 10,693 homozygotes. There are 15,252 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 0.49 (10693 hom., 15252 hem., cov: 22)
• Consequence: DIAPH2 NM_006729.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIAPH2	NM_006729.5	c.587+5802C>T		intron_variant		ENST00000324765.13
DIAPH2	NM_007309.4	c.587+5802C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIAPH2	ENST00000324765.13	c.587+5802C>T		intron_variant		1	NM_006729.5	A2
DIAPH2	ENST00000373049.8	c.587+5802C>T		intron_variant		1		P3

Frequencies

GnomAD3 genomes AF: 0.487 AC: 53329 AN: 109580 Hom.: 10701 Cov.: 22 AF XY: 0.477 AC XY: 15214 AN XY: 31912

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.487 AC: 53354 AN: 109628 Hom.: 10693 Cov.: 22 AF XY: 0.477 AC XY: 15252 AN XY: 31970

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.466

Alfa AF: 0.384 Hom.: 34928

Bravo AF: 0.514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.13
Dann	Benign	0.55

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: rs233214; hg19: chrX-96142519;