rs6051702

chr20-3271278-A-C

Variant summary

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

The NM_001009984.3(DNAAF9):c.2651-716T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,070 control chromosomes in the GnomAD database, including 3,059 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 0.19 (3059 hom., cov: 31)
• Consequence: DNAAF9 NM_001009984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAAF9	NM_001009984.3	c.2651-716T>G		intron_variant		ENST00000252032.10
DNAAF9	XM_005260684.5	c.2648-716T>G		intron_variant
DNAAF9	XM_005260687.6	c.896-716T>G		intron_variant
DNAAF9	XM_011529208.4	c.896-716T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAAF9	ENST00000252032.10	c.2651-716T>G		intron_variant		5	NM_001009984.3	P1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29297 AN: 151952 Hom.: 3056 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.193 AC: 29304 AN: 152070 Hom.: 3059 Cov.: 31 AF XY: 0.188 AC XY: 13960 AN XY: 74348

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0934

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.191

Alfa AF: 0.188 Hom.: 1251

Bravo AF: 0.201

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.3
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs6051702; hg19: chr20-3251924;