rs2019061

chr22-18975827-G-A

Variant summary

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

The NR_110533.2(DGCR5):n.191+5169G>A variant causes a intron, non coding transcript 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 NR_110533.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.956

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGCR5	NR_110533.2	n.191+5169G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGCR5	ENST00000421572.2	n.144+5169G>A		intron_variant, non_coding_transcript_variant		2
DGCR5	ENST00000438934.5	n.145+5169G>A		intron_variant, non_coding_transcript_variant		5
DGCR5	ENST00000674913.1	n.150+5169G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.512

Alfa AF: 0.597 Hom.: 13895

Bravo AF: 0.496

Asia WGS AF: 0.418 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	8.2
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2019061; hg19: chr22-18963340;