chr7-30919387-T-C

Position:

• chr7-30919387-T-C

Variant summary

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

The NM_198098.4(AQP1):​c.385-2679T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,998 control chromosomes in the GnomAD database, including 15,333 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 0.41 (15333 hom., cov: 32)
• Consequence: AQP1 NM_198098.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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]

ENSG00000250424 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AQP1	NM_198098.4	c.385-2679T>C		intron_variant		ENST00000311813.11	NP_932766.1
AQP1	NM_001329872.2	c.385-2679T>C		intron_variant			NP_001316801.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AQP1	ENST00000311813.11	c.385-2679T>C		intron_variant		1	NM_198098.4	ENSP00000311165.4
ENSG00000250424	ENST00000509504.2	c.922-2679T>C		intron_variant		5		ENSP00000421315.2

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62835 AN: 151880 Hom.: 15302 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.414 AC: 62919 AN: 151998 Hom.: 15333 Cov.: 32 AF XY: 0.417 AC XY: 30996 AN XY: 74318

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.390

Alfa AF: 0.310 Hom.: 11364

Bravo AF: 0.429

Asia WGS AF: 0.418 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.82

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: rs17159702; hg19: chr7-30959002;