rs2781665

chr6-131572107-A-T

Variant summary

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

The ENST00000672233.1(ARG1):c.77-7004A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,980 control chromosomes in the GnomAD database, including 13,103 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 0.40 (13103 hom., cov: 32)
• Consequence: ARG1 ENST00000672233.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

ARG1 (HGNC:663): (arginase 1) Arginase catalyzes the hydrolysis of arginine to ornithine and urea. At least two isoforms of mammalian arginase exist (types I and II) which differ in their tissue distribution, subcellular localization, immunologic crossreactivity and physiologic function. The type I isoform encoded by this gene, is a cytosolic enzyme and expressed predominantly in the liver as a component of the urea cycle. Inherited deficiency of this enzyme results in argininemia, an autosomal recessive disorder characterized by hyperammonemia. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARG1	ENST00000672233.1	c.77-7004A>T		intron_variant
ARG1	ENST00000673234.1	c.77-4556A>T		intron_variant, NMD_transcript_variant
ARG1	ENST00000672052.1	n.305-4556A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60439 AN: 151862 Hom.: 13076 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.398 AC: 60517 AN: 151980 Hom.: 13103 Cov.: 32 AF XY: 0.400 AC XY: 29730 AN XY: 74274

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.376

Alfa AF: 0.358 Hom.: 1273

Bravo AF: 0.410

Asia WGS AF: 0.341 AC: 1189 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.9
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2781665; hg19: chr6-131893247; COSMIC: COSV51581727;