rs6037541

Positions:

• chr20-3307057-G-C
• chr20-3307057-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.1679-2514C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 984,270 control chromosomes in the GnomAD database, including 28,754 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 (5352 hom., cov: 32)
  • Exomes 𝑓: 0.24 (23402 hom.)
• Consequence: DNAAF9 NM_001009984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAAF9	NM_001009984.3	c.1679-2514C>G		intron_variant		ENST00000252032.10	NP_001009984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAAF9	ENST00000252032.10	c.1679-2514C>G		intron_variant		5	NM_001009984.3	ENSP00000252032	P1
DNAAF9	ENST00000619760.1	n.445-2514C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38013 AN: 152024 Hom.: 5341 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.236

GnomAD4 exome AF: 0.236 AC: 196251 AN: 832128 Hom.: 23402 Cov.: 30 AF XY: 0.235 AC XY: 90299 AN XY: 384302

Gnomad4 AFR exome AF: 0.383

Gnomad4 AMR exome AF: 0.178

Gnomad4 ASJ exome AF: 0.194

Gnomad4 EAS exome AF: 0.183

Gnomad4 SAS exome AF: 0.184

Gnomad4 FIN exome AF: 0.138

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.227

GnomAD4 genome AF: 0.250 AC: 38054 AN: 152142 Hom.: 5352 Cov.: 32 AF XY: 0.244 AC XY: 18145 AN XY: 74390

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.233

Alfa AF: 0.237 Hom.: 545

Bravo AF: 0.261

Asia WGS AF: 0.179 AC: 620 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	0.52
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs6037541; hg19: chr20-3287704;