5-145859556-G-C

Position:

• chr5-145859556-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001080516.2(GRXCR2):​c.*177C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 621,348 control chromosomes in the GnomAD database, including 227,048 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.88 (59085 hom., cov: 32)
  • Exomes 𝑓: 0.84 (167963 hom.)
• Consequence: GRXCR2 NM_001080516.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.738

Genes affected

GRXCR2 (HGNC:33862): (glutaredoxin and cysteine rich domain containing 2) This gene encodes a protein containing a glutaredoxin domain, which functions in protein S-glutathionylation. A mutation in this gene was found in a family with autoosomal recessive nonsyndromic sensorineural deafness-101. [provided by RefSeq, Jun 2014]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 5-145859556-G-C is Benign according to our data. Variant chr5-145859556-G-C is described in ClinVar as [Benign]. Clinvar id is 1249155.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRXCR2	NM_001080516.2	c.*177C>G		3_prime_UTR_variant	3/3	ENST00000377976.3	NP_001073985.1
GRXCR2	XM_017009708.2	c.*177C>G		3_prime_UTR_variant	3/3		XP_016865197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRXCR2	ENST00000377976.3	c.*177C>G		3_prime_UTR_variant	3/3	2	NM_001080516.2	ENSP00000367214	P1
GRXCR2	ENST00000639411.1	c.*177C>G		3_prime_UTR_variant	4/4	5		ENSP00000491860

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133660 AN: 152126 Hom.: 59026 Cov.: 32

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.862

GnomAD4 exome AF: 0.845 AC: 396191 AN: 469104 Hom.: 167963 Cov.: 4 AF XY: 0.841 AC XY: 207267 AN XY: 246332

Gnomad4 AFR exome AF: 0.968

Gnomad4 AMR exome AF: 0.907

Gnomad4 ASJ exome AF: 0.869

Gnomad4 EAS exome AF: 0.964

Gnomad4 SAS exome AF: 0.819

Gnomad4 FIN exome AF: 0.861

Gnomad4 NFE exome AF: 0.821

Gnomad4 OTH exome AF: 0.853

GnomAD4 genome AF: 0.879 AC: 133774 AN: 152244 Hom.: 59085 Cov.: 32 AF XY: 0.880 AC XY: 65523 AN XY: 74426

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.860

Alfa AF: 0.858 Hom.: 7065

Bravo AF: 0.886

Asia WGS AF: 0.899 AC: 3127 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs432793; hg19: chr5-145239119;