rs1055356

Variant names:

• chr15-34855901-T-C
• rs1055356
• NM_014691.3:c.*891A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AQR	NM_014691.3	c.*891A>G		3_prime_UTR_variant	Exon 35 of 35	ENST00000156471.10	NP_055506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AQR	ENST00000156471.10	c.*891A>G		3_prime_UTR_variant	Exon 35 of 35	1	NM_014691.3	ENSP00000156471.5

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.164 AC: 6822 AN: 41518

American (AMR) AF: 0.391 AC: 5977 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1914 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1093 AN: 5172

South Asian (SAS) AF: 0.448 AC: 2164 AN: 4828

European-Finnish (FIN) AF: 0.541 AC: 5716 AN: 10556

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39102 AN: 67992

Other (OTH) AF: 0.452 AC: 949 AN: 2098

Alfa AF: 0.529 Hom.: 37253

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
PhyloP100		0.25
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1055356; hg19: chr15-35148102;