rs9653034

chr18-26659790-G-A

Variant summary

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

The XR_935311.4(LOC102725227):n.104+3956G>A 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 0.582 in 152,020 control chromosomes in the GnomAD database, including 26,282 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 0.58 (26282 hom., cov: 33)
• Consequence: LOC102725227 XR_935311.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

Genes affected

LOC102725227 (HGNC:):

AQP4-AS1 (HGNC:26399): (AQP4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102725227	XR_935311.4	n.104+3956G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP4-AS1	ENST00000579964.6	n.92+3956G>A		intron_variant, non_coding_transcript_variant		5
AQP4-AS1	ENST00000582605.5	n.93+3956G>A		intron_variant, non_coding_transcript_variant		4
AQP4-AS1	ENST00000657709.1	n.98+3956G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88416 AN: 151902 Hom.: 26263 Cov.: 33

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.582 AC: 88482 AN: 152020 Hom.: 26282 Cov.: 33 AF XY: 0.573 AC XY: 42585 AN XY: 74298

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.548

Alfa AF: 0.577 Hom.: 14463

Bravo AF: 0.586

Asia WGS AF: 0.340 AC: 1183 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9653034; hg19: chr18-24239754;