rs6037541

Variant names:

• chr20-3307057-G-C
• rs6037541
• NM_001009984.3:c.1679-2514C>G

Your query was ambiguous. Multiple possible variants found:

• chr20-3307057-G-C
• chr20-3307057-G-T

Variant summary

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

The NM_001009984.3(DNAAF9):​c.1679-2514C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 984,270 control chromosomes in the GnomAD database, including 28,754 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 0.25 (5352 hom., cov: 32)
  • Exomes 𝑓: 0.24 (23402 hom.)
• Consequence: DNAAF9 NM_001009984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001009984.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAAF9	NM_001009984.3	MANE Select	c.1679-2514C>G		intron	N/A	NP_001009984.1	Q5TEA3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAAF9	ENST00000252032.10	TSL:5 MANE Select	c.1679-2514C>G		intron	N/A	ENSP00000252032.9	Q5TEA3
	DNAAF9	ENST00000851200.1		c.1676-2514C>G		intron	N/A	ENSP00000521259.1
	DNAAF9	ENST00000953496.1		c.1679-2514C>G		intron	N/A	ENSP00000623555.1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38013 AN: 152024 Hom.: 5341 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.236

GnomAD4 exome AF: 0.236 AC: 196251 AN: 832128 Hom.: 23402 Cov.: 30 AF XY: 0.235 AC XY: 90299 AN XY: 384302

African (AFR) AF: 0.383 AC: 6040 AN: 15760

American (AMR) AF: 0.178 AC: 175 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 998 AN: 5144

East Asian (EAS) AF: 0.183 AC: 664 AN: 3622

South Asian (SAS) AF: 0.184 AC: 3029 AN: 16450

European-Finnish (FIN) AF: 0.138 AC: 38 AN: 276

Middle Eastern (MID) AF: 0.164 AC: 265 AN: 1620

European-Non Finnish (NFE) AF: 0.235 AC: 178847 AN: 761010

Other (OTH) AF: 0.227 AC: 6195 AN: 27262

GnomAD4 genome AF: 0.250 AC: 38054 AN: 152142 Hom.: 5352 Cov.: 32 AF XY: 0.244 AC XY: 18145 AN XY: 74390

African (AFR) AF: 0.372 AC: 15427 AN: 41472

American (AMR) AF: 0.199 AC: 3038 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3468

East Asian (EAS) AF: 0.190 AC: 981 AN: 5170

South Asian (SAS) AF: 0.174 AC: 839 AN: 4832

European-Finnish (FIN) AF: 0.131 AC: 1384 AN: 10600

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

European-Non Finnish (NFE) AF: 0.220 AC: 14965 AN: 67996

Other (OTH) AF: 0.233 AC: 494 AN: 2116

Alfa AF: 0.237 Hom.: 545

Bravo AF: 0.261

Asia WGS AF: 0.179 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.70
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs6037541; hg19: chr20-3287704;