rs1340

Variant names:

• chr13-99088399-T-A
• rs1340
• XM_047430231.1:c.-457A>T

Your query was ambiguous. Multiple possible variants found:

• chr13-99088399-T-A
• chr13-99088399-T-C
• chr13-99088399-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

DOCK9 (HGNC:14132): (dedicator of cytokinesis 9) Enables cadherin binding activity. Predicted to be involved in positive regulation of GTPase activity. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_047482.1. 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
	DOCK9-DT	NR_047482.1		n.1677T>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DOCK9-DT	ENST00000562781.1	TSL:6	n.581T>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.350 AC: 7 AN: 20

Other (OTH) AF: 0.167 AC: 1 AN: 6

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

African (AFR) AF: 0.296 AC: 12250 AN: 41400

American (AMR) AF: 0.211 AC: 3232 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2207 AN: 5154

South Asian (SAS) AF: 0.426 AC: 2045 AN: 4802

European-Finnish (FIN) AF: 0.314 AC: 3300 AN: 10520

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21501 AN: 67952

Other (OTH) AF: 0.307 AC: 646 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.51
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1340; hg19: chr13-99740653;