chr14-44864823-G-T

Position:

• chr14-44864823-G-T

Variant summary

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

The ENST00000553480.1(DOCK11P1):​n.1425C>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 0.0562 in 823,664 control chromosomes in the GnomAD database, including 1,804 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 0.050 (257 hom., cov: 33)
  • Exomes 𝑓: 0.058 (1547 hom.)
• Consequence: DOCK11P1 ENST00000553480.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.827

Genes affected

DOCK11P1 (HGNC:31719): (dedicator of cytokinesis 11 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DOCK11P1	ENST00000553480.1	n.1425C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0503 AC: 7656 AN: 152080 Hom.: 258 Cov.: 33

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0443

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0540

GnomAD4 exome AF: 0.0576 AC: 38668 AN: 671466 Hom.: 1547 Cov.: 8 AF XY: 0.0598 AC XY: 21698 AN XY: 362800

Gnomad4 AFR exome AF: 0.0467

Gnomad4 AMR exome AF: 0.0528

Gnomad4 ASJ exome AF: 0.0851

Gnomad4 EAS exome AF: 0.127

Gnomad4 SAS exome AF: 0.108

Gnomad4 FIN exome AF: 0.0868

Gnomad4 NFE exome AF: 0.0380

Gnomad4 OTH exome AF: 0.0543

GnomAD4 genome AF: 0.0503 AC: 7663 AN: 152198 Hom.: 257 Cov.: 33 AF XY: 0.0533 AC XY: 3969 AN XY: 74400

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.0440

Gnomad4 ASJ AF: 0.0801

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.0390

Gnomad4 OTH AF: 0.0549

Alfa AF: 0.0318 Hom.: 58

Bravo AF: 0.0483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	3.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483549; hg19: chr14-45334026;