rs3759129

Variant names:

• chr12-49960654-A-C
• rs3759129
• ENST00000550214.2:n.287-1010T>G

Variant summary

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

The ENST00000550214.2(AQP5-AS1):​n.287-1010T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,074 control chromosomes in the GnomAD database, including 1,754 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 0.14 (1754 hom., cov: 31)
• Consequence: AQP5-AS1 ENST00000550214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 41 publications found

Genes affected

AQP5-AS1 (HGNC:55474): (AQP5 and AQP2 antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550214.2. 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
	AQP5-AS1	NR_110589.1		n.259-1010T>G		intron	N/A
	AQP5-AS1	NR_110590.1		n.256+2013T>G		intron	N/A
	AQP5-AS1	NR_110591.1		n.117+2013T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AQP5-AS1	ENST00000550214.2	TSL:2	n.287-1010T>G		intron	N/A
	AQP5-AS1	ENST00000550530.1	TSL:3	n.117+2013T>G		intron	N/A
	AQP5-AS1	ENST00000552379.1	TSL:3	n.256+2013T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21180 AN: 151956 Hom.: 1753 Cov.: 31

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.139 AC: 21200 AN: 152074 Hom.: 1754 Cov.: 31 AF XY: 0.137 AC XY: 10203 AN XY: 74344

African (AFR) AF: 0.0720 AC: 2988 AN: 41488

American (AMR) AF: 0.134 AC: 2052 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3470

East Asian (EAS) AF: 0.0158 AC: 82 AN: 5174

South Asian (SAS) AF: 0.0649 AC: 312 AN: 4808

European-Finnish (FIN) AF: 0.151 AC: 1596 AN: 10588

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12774 AN: 67956

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.171 Hom.: 5657

Bravo AF: 0.138

Asia WGS AF: 0.0930 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3759129;

hg19: chr12-50354437;