rs2862

Variant names:

• chr15-34853352-C-T
• rs2862
• NM_014691.3:c.*3440G>A

Variant summary

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

The NM_014691.3(AQR):​c.*3440G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,854 control chromosomes in the GnomAD database, including 39,605 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 0.72 (39604 hom., cov: 30)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: AQR NM_014691.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 14 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AQR	NM_014691.3	c.*3440G>A		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.*3440G>A		3_prime_UTR_variant	Exon 35 of 35	1	NM_014691.3	ENSP00000156471.5

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109085 AN: 151730 Hom.: 39573 Cov.: 30

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.716

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 3 AN XY: 6

African (AFR) AC: 0 AN: 0

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: 0.750 AC: 3 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.719 AC: 109170 AN: 151848 Hom.: 39604 Cov.: 30 AF XY: 0.715 AC XY: 53092 AN XY: 74212

African (AFR) AF: 0.666 AC: 27540 AN: 41354

American (AMR) AF: 0.620 AC: 9467 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2706 AN: 3466

East Asian (EAS) AF: 0.542 AC: 2793 AN: 5154

South Asian (SAS) AF: 0.766 AC: 3683 AN: 4810

European-Finnish (FIN) AF: 0.773 AC: 8147 AN: 10546

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52421 AN: 67946

Other (OTH) AF: 0.717 AC: 1512 AN: 2110

Alfa AF: 0.748 Hom.: 7933

Bravo AF: 0.701

Asia WGS AF: 0.667 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.8
DANN	Benign	0.63
PhyloP100		-0.14

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: rs2862; hg19: chr15-35145553;