7-30921380-G-A

Position:

• chr7-30921380-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_198098.4(AQP1):​c.385-686G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0576 in 1,405,316 control chromosomes in the GnomAD database, including 3,748 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.091 (882 hom., cov: 33)
  • Exomes 𝑓: 0.054 (2866 hom.)
• Consequence: AQP1 NM_198098.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0810

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 7-30921380-G-A is Benign according to our data. Variant chr7-30921380-G-A is described in ClinVar as [Benign]. Clinvar id is 1223959.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AQP1	NM_198098.4	c.385-686G>A		intron_variant		ENST00000311813.11
AQP1	NM_001329872.2	c.385-686G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP1	ENST00000311813.11	c.385-686G>A		intron_variant		1	NM_198098.4	P1

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13776 AN: 152080 Hom.: 880 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.0872

GnomAD4 exome AF: 0.0536 AC: 67218 AN: 1253118 Hom.: 2866 Cov.: 30 AF XY: 0.0548 AC XY: 33035 AN XY: 603072

Gnomad4 AFR exome AF: 0.166

Gnomad4 AMR exome AF: 0.0650

Gnomad4 ASJ exome AF: 0.0575

Gnomad4 EAS exome AF: 0.221

Gnomad4 SAS exome AF: 0.105

Gnomad4 FIN exome AF: 0.0450

Gnomad4 NFE exome AF: 0.0414

Gnomad4 OTH exome AF: 0.0682

GnomAD4 genome AF: 0.0905 AC: 13781 AN: 152198 Hom.: 882 Cov.: 33 AF XY: 0.0926 AC XY: 6894 AN XY: 74414

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0695

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0497

Gnomad4 NFE AF: 0.0448

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0784 Hom.: 110

Bravo AF: 0.0953

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.67

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: rs2267720; hg19: chr7-30960995;