rs17249437

Positions:

• chr14-67634170-T-C

Variant summary

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

The NM_001172.4(ARG2):​c.185-8016T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,052 control chromosomes in the GnomAD database, including 15,208 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 (15208 hom., cov: 31)
• Consequence: ARG2 NM_001172.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

ARG2 (HGNC:664): (arginase 2) Arginase catalyzes the hydrolysis of arginine to ornithine and urea. At least two isoforms of mammalian arginase exists (types I and II) which differ in their tissue distribution, subcellular localization, immunologic crossreactivity and physiologic function. The type II isoform encoded by this gene, is located in the mitochondria and expressed in extra-hepatic tissues, especially kidney. The physiologic role of this isoform is poorly understood; it is thought to play a role in nitric oxide and polyamine metabolism. Transcript variants of the type II gene resulting from the use of alternative polyadenylation sites have been described. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARG2	NM_001172.4	c.185-8016T>C		intron_variant		ENST00000261783.4	NP_001163.1
LOC124903331	XR_007064218.1	n.1121+4423A>G		intron_variant, non_coding_transcript_variant
GPHN	XM_047430879.1	c.1313-101025T>C		intron_variant			XP_047286835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARG2	ENST00000261783.4	c.185-8016T>C		intron_variant		1	NM_001172.4	ENSP00000261783	P1
	ENST00000662787.1	n.1083+4423A>G		intron_variant, non_coding_transcript_variant
ARG2	ENST00000556491.1	n.183-8016T>C		intron_variant, non_coding_transcript_variant		5
ARG2	ENST00000557120.5	n.227-8016T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61885 AN: 151934 Hom.: 15157 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.408 AC: 62014 AN: 152052 Hom.: 15208 Cov.: 31 AF XY: 0.407 AC XY: 30248 AN XY: 74338

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.428

Alfa AF: 0.350 Hom.: 1454

Bravo AF: 0.435

Asia WGS AF: 0.435 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.63

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: rs17249437; hg19: chr14-68100887;