rs17043990

Positions:

• chr3-72831319-T-C
• chr3-72831319-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_018130.3(SHQ1):​c.599+1050A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0298 in 152,290 control chromosomes in the GnomAD database, including 197 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 0.030 (197 hom., cov: 32)
• Consequence: SHQ1 NM_018130.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770

Genes affected

SHQ1 (HGNC:25543): (SHQ1, H/ACA ribonucleoprotein assembly factor) SHQ1 assists in the assembly of H/ACA-box ribonucleoproteins that function in the processing of ribosomal RNAs, modification of spliceosomal small nuclear RNAs, and stabilization of telomerase (see MIM 602322) (Grozdanov et al., 2009 [PubMed 19383767]).[supplied by OMIM, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SHQ1	NM_018130.3	c.599+1050A>G		intron_variant		ENST00000325599.13	NP_060600.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SHQ1	ENST00000325599.13	c.599+1050A>G		intron_variant		1	NM_018130.3	ENSP00000315182.8
SHQ1	ENST00000463369.5	c.515+1050A>G		intron_variant		2		ENSP00000417452.1
SHQ1	ENST00000444040.6	n.*476+1050A>G		intron_variant		2		ENSP00000402447.2

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4532 AN: 152172 Hom.: 197 Cov.: 32

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00328

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0298 AC: 4539 AN: 152290 Hom.: 197 Cov.: 32 AF XY: 0.0289 AC XY: 2154 AN XY: 74466

Gnomad4 AFR AF: 0.0893

Gnomad4 AMR AF: 0.0195

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00328

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0102 Hom.: 51

Bravo AF: 0.0336

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	9.9
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17043990; hg19: chr3-72880470;