15-34962395-A-G

Variant names:

• chr15-34962395-A-G
• rs2060810
• NM_014691.3:c.133-1581T>C

Variant summary

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

The NM_014691.3(AQR):​c.133-1581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,070 control chromosomes in the GnomAD database, including 30,760 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 0.61 (30760 hom., cov: 31)
• Consequence: AQR NM_014691.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014691.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AQR	NM_014691.3	MANE Select	c.133-1581T>C		intron	N/A	NP_055506.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AQR	ENST00000156471.10	TSL:1 MANE Select	c.133-1581T>C		intron	N/A	ENSP00000156471.5
	AQR	ENST00000875393.1		c.133-1581T>C		intron	N/A	ENSP00000545452.1
	AQR	ENST00000945427.1		c.76-1581T>C		intron	N/A	ENSP00000615486.1

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93048 AN: 151950 Hom.: 30751 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.612 AC: 93088 AN: 152070 Hom.: 30760 Cov.: 31 AF XY: 0.614 AC XY: 45677 AN XY: 74356

African (AFR) AF: 0.349 AC: 14479 AN: 41448

American (AMR) AF: 0.575 AC: 8791 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2391 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3406 AN: 5180

South Asian (SAS) AF: 0.750 AC: 3622 AN: 4828

European-Finnish (FIN) AF: 0.787 AC: 8319 AN: 10570

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49957 AN: 67982

Other (OTH) AF: 0.624 AC: 1315 AN: 2108

Alfa AF: 0.695 Hom.: 23815

Bravo AF: 0.582

Asia WGS AF: 0.676 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.39
PhyloP100		-2.3
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: rs2060810; hg19: chr15-35254596;