rs17810548

Positions:

• chr22-19016425-C-T

Variant summary

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

The NR_110533.2(DGCR5):​n.895+1919C>T 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 0.144 in 151,982 control chromosomes in the GnomAD database, including 1,565 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 0.14 (1565 hom., cov: 32)
• Consequence: DGCR5 NR_110533.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGCR5	NR_110533.2	n.895+1919C>T		intron_variant, non_coding_transcript_variant
DGCR5	NR_024159.2	n.752-872C>T		intron_variant, non_coding_transcript_variant
DGCR5	NR_026651.2	n.751+1919C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGCR5	ENST00000675214.1	n.375-872C>T		intron_variant, non_coding_transcript_variant
DGCR5	ENST00000675671.1	n.1064-872C>T		intron_variant, non_coding_transcript_variant
DGCR5	ENST00000675978.1	n.917-872C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21914 AN: 151864 Hom.: 1562 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.144 AC: 21943 AN: 151982 Hom.: 1565 Cov.: 32 AF XY: 0.145 AC XY: 10776 AN XY: 74288

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0714

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.152

Alfa AF: 0.147 Hom.: 1745

Bravo AF: 0.149

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.49
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17810548; hg19: chr22-19003938;