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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new If you want to explore the variant's impact on the transcript ENST00000440005.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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).

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

Gene	Transcript	HGVSc	Effect	Exon Rank
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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
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.:

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over