20-3256586-C-T

Variant names:

• chr20-3256586-C-T
• rs3310
• NM_001009984.3:c.3056-375G>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.3056-375G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,998 control chromosomes in the GnomAD database, including 3,151 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 0.20 (3151 hom., cov: 32)
• Consequence: DNAAF9 NM_001009984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 8 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 = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAAF9	NM_001009984.3	c.3056-375G>A		intron_variant	Intron 33 of 36	ENST00000252032.10	NP_001009984.1
DNAAF9	XM_005260684.5	c.3053-375G>A		intron_variant	Intron 33 of 36		XP_005260741.1
DNAAF9	XM_005260687.6	c.1301-375G>A		intron_variant	Intron 14 of 17		XP_005260744.1
DNAAF9	XM_011529208.4	c.1301-375G>A		intron_variant	Intron 14 of 17		XP_011527510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAAF9	ENST00000252032.10	c.3056-375G>A		intron_variant	Intron 33 of 36	5	NM_001009984.3	ENSP00000252032.9

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29901 AN: 151880 Hom.: 3148 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.197 AC: 29909 AN: 151998 Hom.: 3151 Cov.: 32 AF XY: 0.193 AC XY: 14359 AN XY: 74320

African (AFR) AF: 0.246 AC: 10187 AN: 41402

American (AMR) AF: 0.178 AC: 2720 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3466

East Asian (EAS) AF: 0.165 AC: 852 AN: 5174

South Asian (SAS) AF: 0.154 AC: 744 AN: 4822

European-Finnish (FIN) AF: 0.114 AC: 1209 AN: 10586

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12951 AN: 67974

Other (OTH) AF: 0.194 AC: 410 AN: 2108

Alfa AF: 0.188 Hom.: 1374

Bravo AF: 0.204

Asia WGS AF: 0.139 AC: 481 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	4.4
DANN	Benign	0.37
PhyloP100		-0.28
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: rs3310; hg19: chr20-3237232;