15-55485440-T-G

Position:

• chr15-55485440-T-G

Variant summary

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

The NM_130810.4(DNAAF4):​c.405+5683A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,120 control chromosomes in the GnomAD database, including 5,832 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 0.25 (5832 hom., cov: 31)
• Consequence: DNAAF4 NM_130810.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

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:43019): (DNAAF4-CCPG1 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring dyslexia susceptibility 1 candidate 1 (DYX1C1) and cell cycle progression 1 (CCPG1) genes on chromosome 15. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAAF4	NM_130810.4	c.405+5683A>C		intron_variant		ENST00000321149.7	NP_570722.2
DNAAF4	NM_001033560.2	c.405+5683A>C		intron_variant			NP_001028732.1
DNAAF4	NM_001033559.3	c.405+5683A>C		intron_variant			NP_001028731.1
DNAAF4-CCPG1	NR_037923.1	n.660+5683A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAAF4	ENST00000321149.7	c.405+5683A>C		intron_variant		1	NM_130810.4	ENSP00000323275.3

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38505 AN: 152004 Hom.: 5834 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.253 AC: 38499 AN: 152120 Hom.: 5832 Cov.: 31 AF XY: 0.250 AC XY: 18596 AN XY: 74360

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0662

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.255

Alfa AF: 0.208 Hom.: 529

Bravo AF: 0.238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.76

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: rs11629841; hg19: chr15-55777638;