chr20-3378656-C-T

Variant names:

• chr20-3378656-C-T
• rs6115865
• NM_001009984.3:c.284-2354G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009984.3(DNAAF9):​c.284-2354G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,924 control chromosomes in the GnomAD database, including 10,317 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 0.35 (10317 hom., cov: 31)
• Consequence: DNAAF9 NM_001009984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 14 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAAF9	NM_001009984.3	c.284-2354G>A		intron_variant	Intron 3 of 36	ENST00000252032.10	NP_001009984.1
DNAAF9	XM_005260684.5	c.284-2354G>A		intron_variant	Intron 3 of 36		XP_005260741.1
DNAAF9	XM_047440081.1	c.284-2354G>A		intron_variant	Intron 3 of 25		XP_047296037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAAF9	ENST00000252032.10	c.284-2354G>A		intron_variant	Intron 3 of 36	5	NM_001009984.3	ENSP00000252032.9

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53566 AN: 151804 Hom.: 10303 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.353 AC: 53610 AN: 151924 Hom.: 10317 Cov.: 31 AF XY: 0.346 AC XY: 25725 AN XY: 74264

African (AFR) AF: 0.510 AC: 21108 AN: 41384

American (AMR) AF: 0.290 AC: 4425 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1765 AN: 5156

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4814

European-Finnish (FIN) AF: 0.238 AC: 2514 AN: 10568

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20684 AN: 67968

Other (OTH) AF: 0.341 AC: 718 AN: 2108

Alfa AF: 0.319 Hom.: 33773

Bravo AF: 0.364

Asia WGS AF: 0.281 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.029
DANN	Benign	0.52
PhyloP100		-1.9
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: rs6115865; hg19: chr20-3359303;