rs1340

Positions:

• chr13-99088399-T-A
• chr13-99088399-T-C
• chr13-99088399-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.1677T>A 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 0.307 in 151,918 control chromosomes in the GnomAD database, including 7,493 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 0.31 (7491 hom., cov: 31)
  • Exomes 𝑓: 0.30 (2 hom.)
• Consequence: DOCK9-DT NR_047482.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK9-DT	NR_047482.1	n.1677T>A		non_coding_transcript_exon_variant	1/1
DOCK9	XM_047430231.1	c.-457A>T		5_prime_UTR_variant	1/56		XP_047286187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DOCK9-DT	ENST00000562781.1	n.581T>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46565 AN: 151768 Hom.: 7469 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.300 AC: 9 AN: 30 Hom.: 2 Cov.: 0 AF XY: 0.292 AC XY: 7 AN XY: 24

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.350

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.307 AC: 46621 AN: 151888 Hom.: 7491 Cov.: 31 AF XY: 0.309 AC XY: 22917 AN XY: 74208

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.307

Alfa AF: 0.178 Hom.: 360

Bravo AF: 0.294

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1340; hg19: chr13-99740653;