rs17810548

Variant names:

• chr22-19016425-C-T
• rs17810548
• ENST00000440005.6:n.838+1919C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440005.6(DGCR5):​n.838+1919C>T variant causes a intron 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 ENST00000440005.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DGCR5	NR_024159.2	n.752-872C>T		intron_variant	Intron 4 of 4
DGCR5	NR_026651.2	n.751+1919C>T		intron_variant	Intron 4 of 4
DGCR5	NR_110533.2	n.895+1919C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGCR5	ENST00000440005.6	n.838+1919C>T		intron_variant	Intron 5 of 5	1
DGCR5	ENST00000609630.2	n.773-872C>T		intron_variant	Intron 6 of 6	6
DGCR5	ENST00000675214.1	n.375-872C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.159 AC: 6587 AN: 41424

American (AMR) AF: 0.162 AC: 2468 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3468

East Asian (EAS) AF: 0.0714 AC: 370 AN: 5180

South Asian (SAS) AF: 0.140 AC: 674 AN: 4808

European-Finnish (FIN) AF: 0.111 AC: 1169 AN: 10576

Middle Eastern (MID) AF: 0.193 AC: 56 AN: 290

European-Non Finnish (NFE) AF: 0.140 AC: 9488 AN: 67956

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.147 Hom.: 2518

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
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17810548; hg19: chr22-19003938;