rs5046

Positions:

• chr1-230714652-G-A

Variant summary

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

The ENST00000412344.1(ENSG00000244137):​n.381-3799C>T 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 0.12 in 152,210 control chromosomes in the GnomAD database, including 1,110 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 0.12 (1110 hom., cov: 32)
• Consequence: ENST00000412344.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

Genes affected

(HGNC:):

AGT (HGNC:333): (angiotensinogen) The protein encoded by this gene, pre-angiotensinogen or angiotensinogen precursor, is expressed in the liver and is cleaved by the enzyme renin in response to lowered blood pressure. The resulting product, angiotensin I, is then cleaved by angiotensin converting enzyme (ACE) to generate the physiologically active enzyme angiotensin II. The protein is involved in maintaining blood pressure, body fluid and electrolyte homeostasis, and in the pathogenesis of essential hypertension and preeclampsia. Mutations in this gene are associated with susceptibility to essential hypertension, and can cause renal tubular dysgenesis, a severe disorder of renal tubular development. Defects in this gene have also been associated with non-familial structural atrial fibrillation, and inflammatory bowel disease. [provided by RefSeq, Nov 2019]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGT	NM_001382817.3	c.-30-3799C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412344.1	n.381-3799C>T		intron_variant, non_coding_transcript_variant		3
AGT	ENST00000681269.1	c.-30-3799C>T		intron_variant				P1
AGT	ENST00000679738.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18196 AN: 152092 Hom.: 1107 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.120 AC: 18206 AN: 152210 Hom.: 1110 Cov.: 32 AF XY: 0.122 AC XY: 9107 AN XY: 74428

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0859

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.111

Alfa AF: 0.118 Hom.: 230

Bravo AF: 0.117

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5046; hg19: chr1-230850398;