7-30924207-G-C

Position:

• chr7-30924207-G-C

Variant summary

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

The NM_198098.4(AQP1):​c.*578G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 939,506 control chromosomes in the GnomAD database, including 86,219 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 0.51 (23030 hom., cov: 33)
  • Exomes 𝑓: 0.39 (63189 hom.)
• Consequence: AQP1 NM_198098.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

Genes affected

AQP1 (HGNC:633): (aquaporin 1 (Colton blood group)) This gene encodes a small integral membrane protein with six bilayer spanning domains that functions as a water channel protein. This protein permits passive transport of water along an osmotic gradient. This gene is a possible candidate for disorders involving imbalance in ocular fluid movement. [provided by RefSeq, Aug 2016]

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 = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AQP1	NM_198098.4	c.*578G>C		3_prime_UTR_variant	4/4	ENST00000311813.11
AQP1	NM_001329872.2	c.*198G>C		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP1	ENST00000311813.11	c.*578G>C		3_prime_UTR_variant	4/4	1	NM_198098.4	P1
AQP1	ENST00000441328.7	n.522G>C		non_coding_transcript_exon_variant	2/2	1
AQP1	ENST00000652696.1	c.*405G>C		3_prime_UTR_variant	5/5			P1
AQP1	ENST00000652692.1	c.*24+554G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77983 AN: 152030 Hom.: 22981 Cov.: 33

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.496

GnomAD4 exome AF: 0.395 AC: 310736 AN: 787358 Hom.: 63189 Cov.: 10 AF XY: 0.394 AC XY: 148346 AN XY: 376308

Gnomad4 AFR exome AF: 0.857

Gnomad4 AMR exome AF: 0.430

Gnomad4 ASJ exome AF: 0.397

Gnomad4 EAS exome AF: 0.348

Gnomad4 SAS exome AF: 0.423

Gnomad4 FIN exome AF: 0.332

Gnomad4 NFE exome AF: 0.382

Gnomad4 OTH exome AF: 0.410

GnomAD4 genome AF: 0.513 AC: 78090 AN: 152148 Hom.: 23030 Cov.: 33 AF XY: 0.510 AC XY: 37915 AN XY: 74386

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.497

Alfa AF: 0.446 Hom.: 2320

Bravo AF: 0.534

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.75
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs1049305; hg19: chr7-30963822;