chr20-3340943-T-C

Variant names:

• chr20-3340943-T-C
• rs6051762
• NM_001009984.3:c.846-304A>G

Variant summary

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

The NM_001009984.3(DNAAF9):​c.846-304A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,116 control chromosomes in the GnomAD database, including 2,267 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 0.17 (2267 hom., cov: 31)
• Consequence: DNAAF9 NM_001009984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAAF9	NM_001009984.3	c.846-304A>G		intron_variant	Intron 9 of 36	ENST00000252032.10	NP_001009984.1
DNAAF9	XM_005260684.5	c.846-304A>G		intron_variant	Intron 9 of 36		XP_005260741.1
DNAAF9	XM_047440081.1	c.846-304A>G		intron_variant	Intron 9 of 25		XP_047296037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAAF9	ENST00000252032.10	c.846-304A>G		intron_variant	Intron 9 of 36	5	NM_001009984.3	ENSP00000252032.9

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25210 AN: 151998 Hom.: 2265 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.166 AC: 25212 AN: 152116 Hom.: 2267 Cov.: 31 AF XY: 0.161 AC XY: 11995 AN XY: 74360

African (AFR) AF: 0.148 AC: 6128 AN: 41496

American (AMR) AF: 0.164 AC: 2507 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3472

East Asian (EAS) AF: 0.147 AC: 758 AN: 5174

South Asian (SAS) AF: 0.154 AC: 741 AN: 4826

European-Finnish (FIN) AF: 0.0930 AC: 985 AN: 10588

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12890 AN: 67962

Other (OTH) AF: 0.174 AC: 368 AN: 2110

Alfa AF: 0.179 Hom.: 1230

Bravo AF: 0.171

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.61
PhyloP100		0.065
Mutation Taster		=300/0	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: rs6051762; hg19: chr20-3321590;