rs1927568

Positions:

• chr13-99087863-T-C
• chr13-99087863-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_047482.1(DOCK9-DT):​n.1141T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,086 control chromosomes in the GnomAD database, including 6,359 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 0.28 (6358 hom., cov: 33)
  • Exomes 𝑓: 0.24 (1 hom.)
• Consequence: DOCK9-DT NR_047482.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

DOCK9-DT (HGNC:43696): (DOCK9 divergent transcript)

DOCK9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOCK9-DT	NR_047482.1	n.1141T>C		non_coding_transcript_exon_variant	1/1
DOCK9	XM_047430231.1	c.80A>G	p.His27Arg	missense_variant	1/56

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOCK9-DT	ENST00000562781.1	n.45T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42585 AN: 151896 Hom.: 6338 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.276

GnomAD4 exome AF: 0.236 AC: 17 AN: 72 Hom.: 1 Cov.: 0 AF XY: 0.207 AC XY: 12 AN XY: 58

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.259

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.280 AC: 42635 AN: 152014 Hom.: 6358 Cov.: 33 AF XY: 0.282 AC XY: 20981 AN XY: 74292

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.277

Alfa AF: 0.273 Hom.: 7326

Bravo AF: 0.270

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1927568; hg19: chr13-99740117; COSMIC: COSV59644974;