rs1055356

chr15-34855901-T-C

Variant summary

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

The NM_014691.3(AQR):c.*891A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,126 control chromosomes in the GnomAD database, including 16,141 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 0.42 (16141 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: AQR NM_014691.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

Genes affected

AQR (HGNC:29513): (aquarius intron-binding spliceosomal factor) Enables 3'-5' RNA helicase activity and single-stranded RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of U2-type catalytic step 2 spliceosome. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AQR	NM_014691.3	c.*891A>G		3_prime_UTR_variant	35/35	ENST00000156471.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQR	ENST00000156471.10	c.*891A>G		3_prime_UTR_variant	35/35	1	NM_014691.3	P1

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64327 AN: 152010 Hom.: 16149 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.452

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.423 AC: 64307 AN: 152118 Hom.: 16141 Cov.: 32 AF XY: 0.420 AC XY: 31239 AN XY: 74364

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.452

Alfa AF: 0.543 Hom.: 30561

Bravo AF: 0.397

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.7
Dann	Benign	0.82
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1055356; hg19: chr15-35148102;