rs3759129

Positions:

• chr12-49960654-A-C

Variant summary

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

The NR_110591.1(AQP5-AS1):​n.117+2013T>G variant causes a intron, non coding transcript 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 NR_110591.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AQP5-AS1	NR_110591.1	n.117+2013T>G		intron_variant, non_coding_transcript_variant
AQP5-AS1	NR_110589.1	n.259-1010T>G		intron_variant, non_coding_transcript_variant
AQP5-AS1	NR_110590.1	n.256+2013T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP5-AS1	ENST00000550530.1	n.117+2013T>G		intron_variant, non_coding_transcript_variant		3
AQP5-AS1	ENST00000550214.1	n.259-1010T>G		intron_variant, non_coding_transcript_variant		2
AQP5-AS1	ENST00000552379.1	n.256+2013T>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0720

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.0158

Gnomad4 SAS AF: 0.0649

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.149

Alfa AF: 0.173 Hom.: 1524

Bravo AF: 0.138

Asia WGS AF: 0.0930 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759129; hg19: chr12-50354437;