chr14-67646576-G-A

Variant names:

• chr14-67646576-G-A
• rs742869
• NM_001172.4:c.523-68G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001172.4(ARG2):​c.523-68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,278,946 control chromosomes in the GnomAD database, including 202,436 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 0.45 (17871 hom., cov: 32)
  • Exomes 𝑓: 0.56 (184565 hom.)
• Consequence: ARG2 NM_001172.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

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]

GPHN (HGNC:15465): (gephyrin) This gene encodes a neuronal assembly protein that anchors inhibitory neurotransmitter receptors to the postsynaptic cytoskeleton via high affinity binding to a receptor subunit domain and tubulin dimers. In nonneuronal tissues, the encoded protein is also required for molybdenum cofactor biosynthesis. Mutations in this gene may be associated with the neurological condition hyperplexia and also lead to molybdenum cofactor deficiency. Numerous alternatively spliced transcript variants encoding different isoforms have been described; however, the full-length nature of all transcript variants is not currently known. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARG2	NM_001172.4	c.523-68G>A		intron_variant	Intron 4 of 7	ENST00000261783.4	NP_001163.1
GPHN	XM_047430879.1	c.1313-88619G>A		intron_variant	Intron 14 of 14		XP_047286835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARG2	ENST00000261783.4	c.523-68G>A		intron_variant	Intron 4 of 7	1	NM_001172.4	ENSP00000261783.3
ARG2	ENST00000557319.1	n.129G>A		non_coding_transcript_exon_variant	Exon 1 of 4	2
ARG2	ENST00000556491.1	n.361-68G>A		intron_variant	Intron 3 of 3	5
ARG2	ENST00000557120.5	n.565-68G>A		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68165 AN: 151952 Hom.: 17875 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.426

GnomAD4 exome AF: 0.560 AC: 630619 AN: 1126876 Hom.: 184565 Cov.: 15 AF XY: 0.556 AC XY: 317790 AN XY: 571476

Gnomad4 AFR exome AF: 0.173 AC: 4593 AN: 26584

Gnomad4 AMR exome AF: 0.378 AC: 15722 AN: 41600

Gnomad4 ASJ exome AF: 0.547 AC: 12069 AN: 22082

Gnomad4 EAS exome AF: 0.279 AC: 10583 AN: 37966

Gnomad4 SAS exome AF: 0.385 AC: 28490 AN: 73908

Gnomad4 FIN exome AF: 0.553 AC: 28503 AN: 51574

Gnomad4 NFE exome AF: 0.615 AC: 503359 AN: 819056

Gnomad4 Remaining exome AF: 0.519 AC: 25448 AN: 49048

GnomAD4 genome AF: 0.448 AC: 68171 AN: 152070 Hom.: 17871 Cov.: 32 AF XY: 0.444 AC XY: 32988 AN XY: 74338

Gnomad4 AFR AF: 0.190 AC: 0.190126 AN: 0.190126

Gnomad4 AMR AF: 0.400 AC: 0.399646 AN: 0.399646

Gnomad4 ASJ AF: 0.558 AC: 0.558025 AN: 0.558025

Gnomad4 EAS AF: 0.302 AC: 0.302245 AN: 0.302245

Gnomad4 SAS AF: 0.363 AC: 0.363448 AN: 0.363448

Gnomad4 FIN AF: 0.560 AC: 0.559603 AN: 0.559603

Gnomad4 NFE AF: 0.609 AC: 0.608835 AN: 0.608835

Gnomad4 OTH AF: 0.421 AC: 0.420853 AN: 0.420853

Alfa AF: 0.548 Hom.: 39528

Bravo AF: 0.423

Asia WGS AF: 0.310 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.58
Mutation Taster		=100/0	polymorphism (auto)

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: rs742869; hg19: chr14-68113293; COSMIC: COSV53619850; COSMIC: COSV53619850;