20-3263803-T-G

Variant names:

• chr20-3263803-T-G
• rs6051693
• NM_001009984.3:c.2873+635A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DNAAF9	NM_001009984.3	c.2873+635A>C		intron_variant	Intron 31 of 36	ENST00000252032.10	NP_001009984.1
DNAAF9	XM_005260684.5	c.2870+635A>C		intron_variant	Intron 31 of 36		XP_005260741.1
DNAAF9	XM_005260687.6	c.1118+635A>C		intron_variant	Intron 12 of 17		XP_005260744.1
DNAAF9	XM_011529208.4	c.1118+635A>C		intron_variant	Intron 12 of 17		XP_011527510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAAF9	ENST00000252032.10	c.2873+635A>C		intron_variant	Intron 31 of 36	5	NM_001009984.3	ENSP00000252032.9

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

African (AFR) AF: 0.340 AC: 14127 AN: 41520

American (AMR) AF: 0.196 AC: 2996 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3466

East Asian (EAS) AF: 0.186 AC: 965 AN: 5180

South Asian (SAS) AF: 0.172 AC: 826 AN: 4812

European-Finnish (FIN) AF: 0.131 AC: 1386 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14971 AN: 67994

Other (OTH) AF: 0.231 AC: 487 AN: 2112

Alfa AF: 0.222 Hom.: 2243

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
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6051693; hg19: chr20-3244449;