Genetic Variant DGCR5:n.685-122G>C (chr22-19014231-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0530

Publications

0 publications found

Variant links:

Genes affected

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

DGCR5 links:

ENSG00000283366 (HGNC:):

ENSG00000283366 links:

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ACMG classification

Classification was made for transcript

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
DGCR5	NR_024159.2 link	n.598-122G>C	intron_variant	Intron 3 of 4
DGCR5	NR_026651.2 link	n.598-122G>C	intron_variant	Intron 3 of 4
DGCR5	NR_110533.2 link	n.742-122G>C	intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DGCR5	ENST00000440005.6 link	n.685-122G>C	intron_variant	Intron 4 of 5	1
DGCR5	ENST00000424407.2 link	n.480-122G>C	intron_variant	Intron 3 of 4	2
DGCR5	ENST00000609630.2 link	n.619-122G>C	intron_variant	Intron 5 of 6	6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

547430

Hom.:

AF XY:

0.00

AC XY:

AN XY:

294168

African (AFR)

AF:

0.00

AC:

AN:

14940

American (AMR)

AF:

0.00

AC:

AN:

31826

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17752

East Asian (EAS)

AF:

0.00

AC:

AN:

29942

South Asian (SAS)

AF:

0.00

AC:

AN:

58106

European-Finnish (FIN)

AF:

0.00

AC:

AN:

45018

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2232

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

318922

Other (OTH)

AF:

0.00

AC:

AN:

28692

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.2

(source)

DANN

Benign

0.35

PhyloP100

0.053

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over