ENST00000440005.6:n.134+5169G>A

Variant names:

• chr22-18975827-G-A
• rs2019061
• ENST00000440005.6:n.134+5169G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440005.6(DGCR5):​n.134+5169G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,026 control chromosomes in the GnomAD database, including 21,733 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 0.51 (21733 hom., cov: 33)
• Consequence: DGCR5 ENST00000440005.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.956
• Publications: 14 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGCR5	NR_002733.3		n.191+5169G>A		intron	N/A
	DGCR5	NR_024159.2		n.191+5169G>A		intron	N/A
	DGCR5	NR_026651.2		n.191+5169G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGCR5	ENST00000440005.6	TSL:1	n.134+5169G>A		intron	N/A
	DGCR5	ENST00000421572.2	TSL:2	n.144+5169G>A		intron	N/A
	DGCR5	ENST00000438934.5	TSL:5	n.145+5169G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77978 AN: 151908 Hom.: 21732 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.516

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.513 AC: 78001 AN: 152026 Hom.: 21733 Cov.: 33 AF XY: 0.511 AC XY: 37950 AN XY: 74300

African (AFR) AF: 0.313 AC: 12960 AN: 41448

American (AMR) AF: 0.505 AC: 7708 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2140 AN: 3464

East Asian (EAS) AF: 0.185 AC: 957 AN: 5162

South Asian (SAS) AF: 0.615 AC: 2962 AN: 4818

European-Finnish (FIN) AF: 0.544 AC: 5750 AN: 10578

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43597 AN: 67958

Other (OTH) AF: 0.512 AC: 1082 AN: 2114

Alfa AF: 0.584 Hom.: 19365

Bravo AF: 0.496

Asia WGS AF: 0.418 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.2
DANN	Benign	0.49
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs2019061; hg19: chr22-18963340;