14-44864823-G-T

Variant names:

• chr14-44864823-G-T
• rs10483549
• ENST00000553480.1:n.1425C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

RRAGAP1-AS1 (HGNC:55445): (RRAGAP1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553480.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DOCK11P1	ENST00000553480.1	TSL:6	n.1425C>A		non_coding_transcript_exon	Exon 1 of 1
	RRAGAP1-AS1	ENST00000715832.1		n.52+32189C>A		intron	N/A
	RRAGAP1-AS1	ENST00000715833.1		n.366-33133C>A		intron	N/A

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

African (AFR) AF: 0.0467 AC: 859 AN: 18388

American (AMR) AF: 0.0528 AC: 2283 AN: 43276

Ashkenazi Jewish (ASJ) AF: 0.0851 AC: 1775 AN: 20864

East Asian (EAS) AF: 0.127 AC: 4596 AN: 36080

South Asian (SAS) AF: 0.108 AC: 7601 AN: 70372

European-Finnish (FIN) AF: 0.0868 AC: 4570 AN: 52662

Middle Eastern (MID) AF: 0.0612 AC: 224 AN: 3658

European-Non Finnish (NFE) AF: 0.0380 AC: 14909 AN: 392086

Other (OTH) AF: 0.0543 AC: 1851 AN: 34080

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

African (AFR) AF: 0.0460 AC: 1911 AN: 41540

American (AMR) AF: 0.0440 AC: 673 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3472

East Asian (EAS) AF: 0.116 AC: 600 AN: 5178

South Asian (SAS) AF: 0.104 AC: 504 AN: 4824

European-Finnish (FIN) AF: 0.0781 AC: 827 AN: 10592

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0390 AC: 2651 AN: 67986

Other (OTH) AF: 0.0549 AC: 116 AN: 2114

Alfa AF: 0.0339 Hom.: 69

Bravo AF: 0.0483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	3.9
DANN	Benign	0.52
PhyloP100		0.83

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10483549;

hg19: chr14-45334026;