rs2078743

Positions:

• chr22-18979346-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.192-8411G>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 0.0983 in 151,850 control chromosomes in the GnomAD database, including 888 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 0.098 (888 hom., cov: 30)
• Consequence: DGCR5 NR_110533.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGCR5	NR_110533.2	n.192-8411G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGCR5	ENST00000421572.2	n.145-6490G>A		intron_variant, non_coding_transcript_variant		2
DGCR5	ENST00000438934.5	n.146-8411G>A		intron_variant, non_coding_transcript_variant		5
DGCR5	ENST00000674913.1	n.151-8411G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0983 AC: 14912 AN: 151732 Hom.: 884 Cov.: 30

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0154

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.0961

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

GnomAD4 genome AF: 0.0983 AC: 14928 AN: 151850 Hom.: 888 Cov.: 30 AF XY: 0.0941 AC XY: 6988 AN XY: 74222

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0668

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.0154

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0905

Gnomad4 OTH AF: 0.0946

Alfa AF: 0.0891 Hom.: 498

Bravo AF: 0.104

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2078743; hg19: chr22-18966859;