rs2422865

Positions:

• chr20-3306495-G-T

Variant summary

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

The NM_001009984.3(DNAAF9):​c.1679-1952C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,064 control chromosomes in the GnomAD database, including 5,346 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 0.26 (5346 hom., cov: 32)
• Consequence: DNAAF9 NM_001009984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.66

Genes affected

DNAAF9 (HGNC:17721): (dynein axonemal assembly factor 9) This gene encodes an uncharacterized protein with a C-terminal coiled-coil region. The gene is located on chromosome 20p13 in a 1.8 Mb region linked to a spinocerebellar ataxia phenotype, but this gene does not appear to be a disease candidate. [provided by RefSeq, Dec 2011]

DNAAF9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAAF9	NM_001009984.3	c.1679-1952C>A		intron_variant		ENST00000252032.10	NP_001009984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAAF9	ENST00000252032.10	c.1679-1952C>A		intron_variant		5	NM_001009984.3	ENSP00000252032.9
DNAAF9	ENST00000619760.1	n.445-1952C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39348 AN: 151944 Hom.: 5342 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.259 AC: 39370 AN: 152064 Hom.: 5346 Cov.: 32 AF XY: 0.266 AC XY: 19746 AN XY: 74324

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.247

Alfa AF: 0.258 Hom.: 647

Bravo AF: 0.255

Asia WGS AF: 0.260 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.033
DANN	Benign	0.77

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: rs2422865; hg19: chr20-3287142;