22-19014231-G-C

Variant names:

• chr22-19014231-G-C
• rs10483098
• ENST00000440005.6:n.685-122G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000440005.6(DGCR5):​n.685-122G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DGCR5 ENST00000440005.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 0 publications found

Genes affected

DGCR5 (HGNC:16757): (DiGeorge syndrome critical region gene 5) Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000283366 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440005.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGCR5	NR_024159.2		n.598-122G>C		intron	N/A
	DGCR5	NR_026651.2		n.598-122G>C		intron	N/A
	DGCR5	NR_110533.2		n.742-122G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGCR5	ENST00000440005.6	TSL:1	n.685-122G>C		intron	N/A
	DGCR5	ENST00000424407.2	TSL:2	n.480-122G>C		intron	N/A
	DGCR5	ENST00000609630.2	TSL:6	n.619-122G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 547430 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 294168

African (AFR) AF: 0.00 AC: 0 AN: 14940

American (AMR) AF: 0.00 AC: 0 AN: 31826

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17752

East Asian (EAS) AF: 0.00 AC: 0 AN: 29942

South Asian (SAS) AF: 0.00 AC: 0 AN: 58106

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45018

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2232

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 318922

Other (OTH) AF: 0.00 AC: 0 AN: 28692

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.35
PhyloP100		0.053

Splicing

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

Other links and lift over

dbSNP: rs10483098; hg19: chr22-19001744;