rs6051693

Positions:

• chr20-3263803-T-G

Variant summary

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

The NM_001009984.3(DNAAF9):​c.2873+635A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,188 control chromosomes in the GnomAD database, including 4,874 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 0.24 (4874 hom., cov: 33)
• Consequence: DNAAF9 NM_001009984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

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=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAAF9	NM_001009984.3	c.2873+635A>C		intron_variant		ENST00000252032.10
DNAAF9	XM_005260684.5	c.2870+635A>C		intron_variant
DNAAF9	XM_005260687.6	c.1118+635A>C		intron_variant
DNAAF9	XM_011529208.4	c.1118+635A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAAF9	ENST00000252032.10	c.2873+635A>C		intron_variant		5	NM_001009984.3	P1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36664 AN: 152070 Hom.: 4870 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.241 AC: 36683 AN: 152188 Hom.: 4874 Cov.: 33 AF XY: 0.235 AC XY: 17499 AN XY: 74390

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.231

Alfa AF: 0.220 Hom.: 1985

Bravo AF: 0.251

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	16
DANN	Benign	0.89

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: rs6051693; hg19: chr20-3244449;