15-55467880-T-C

Position:

• chr15-55467880-T-C

Variant summary

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

The NM_130810.4(DNAAF4):​c.406-719A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,908 control chromosomes in the GnomAD database, including 2,035 homozygotes. 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 0.14 (2035 hom., cov: 32)
• Consequence: DNAAF4 NM_130810.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767

Genes affected

DNAAF4 (HGNC:21493): (dynein axonemal assembly factor 4) This gene encodes a tetratricopeptide repeat domain-containing protein. The encoded protein interacts with estrogen receptors and the heat shock proteins, Hsp70 and Hsp90. An homologous protein in rat has been shown to function in neuronal migration in the developing neocortex. A chromosomal translocation involving this gene is associated with a susceptibility to developmental dyslexia. Mutations in this gene are associated with deficits in reading and spelling. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream cell cycle progression 1 (CCPG1) gene. [provided by RefSeq, Mar 2011]

DNAAF4-CCPG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAAF4	NM_130810.4	c.406-719A>G		intron_variant		ENST00000321149.7
DNAAF4-CCPG1	NR_037923.1	n.661-719A>G		intron_variant, non_coding_transcript_variant
DNAAF4	NM_001033559.3	c.406-719A>G		intron_variant
DNAAF4	NM_001033560.2	c.406-719A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAAF4	ENST00000321149.7	c.406-719A>G		intron_variant		1	NM_130810.4	P1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20933 AN: 151786 Hom.: 2031 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0873

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0109

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0860

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.138 AC: 20964 AN: 151908 Hom.: 2035 Cov.: 32 AF XY: 0.137 AC XY: 10197 AN XY: 74250

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.0872

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0109

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0860

Gnomad4 NFE AF: 0.0861

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0899 Hom.: 1180

Bravo AF: 0.142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.2
DANN	Benign	0.86

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: rs7181999; hg19: chr15-55760078;