rs3736729

Variant names:

• chr6-53514607-A-C
• rs3736729
• NM_001498.4:c.561-110T>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001498.4(GCLC):​c.561-110T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 817,086 control chromosomes in the GnomAD database, including 92,494 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.45 (15500 hom., cov: 32)
  • Exomes 𝑓: 0.48 (76994 hom.)
• Consequence: GCLC NM_001498.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.10
• Publications: 11 publications found

Genes affected

GCLC (HGNC:4311): (glutamate-cysteine ligase catalytic subunit) Glutamate-cysteine ligase, also known as gamma-glutamylcysteine synthetase is the first rate-limiting enzyme of glutathione synthesis. The enzyme consists of two subunits, a heavy catalytic subunit and a light regulatory subunit. This locus encodes the catalytic subunit, while the regulatory subunit is derived from a different gene located on chromosome 1p22-p21. Mutations at this locus have been associated with hemolytic anemia due to deficiency of gamma-glutamylcysteine synthetase and susceptibility to myocardial infarction.[provided by RefSeq, Oct 2010]

GCLC-AS1 (HGNC:56649): (GCLC antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 6-53514607-A-C is Benign according to our data. Variant chr6-53514607-A-C is described in ClinVar as [Benign]. Clinvar id is 1274104.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCLC	NM_001498.4	c.561-110T>G		intron_variant	Intron 4 of 15	ENST00000650454.1	NP_001489.1
GCLC	NM_001197115.2	c.447-110T>G		intron_variant	Intron 3 of 14		NP_001184044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCLC	ENST00000650454.1	c.561-110T>G		intron_variant	Intron 4 of 15		NM_001498.4	ENSP00000497574.1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67728 AN: 151952 Hom.: 15485 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.455

GnomAD4 exome AF: 0.477 AC: 317174 AN: 665014 Hom.: 76994 AF XY: 0.478 AC XY: 171577 AN XY: 358992

African (AFR) AF: 0.355 AC: 6340 AN: 17882

American (AMR) AF: 0.648 AC: 26909 AN: 41512

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 8899 AN: 21120

East Asian (EAS) AF: 0.447 AC: 15590 AN: 34912

South Asian (SAS) AF: 0.519 AC: 35645 AN: 68708

European-Finnish (FIN) AF: 0.448 AC: 22799 AN: 50910

Middle Eastern (MID) AF: 0.486 AC: 2042 AN: 4202

European-Non Finnish (NFE) AF: 0.468 AC: 183149 AN: 391516

Other (OTH) AF: 0.461 AC: 15801 AN: 34252

GnomAD4 genome AF: 0.446 AC: 67768 AN: 152072 Hom.: 15500 Cov.: 32 AF XY: 0.449 AC XY: 33385 AN XY: 74358

African (AFR) AF: 0.362 AC: 15018 AN: 41484

American (AMR) AF: 0.570 AC: 8720 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1418 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2102 AN: 5170

South Asian (SAS) AF: 0.528 AC: 2544 AN: 4820

European-Finnish (FIN) AF: 0.451 AC: 4759 AN: 10552

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31698 AN: 67968

Other (OTH) AF: 0.460 AC: 972 AN: 2112

Alfa AF: 0.469 Hom.: 21724

Bravo AF: 0.450

Asia WGS AF: 0.469 AC: 1630 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3736729; hg19: chr6-53379405; COSMIC: COSV57597419; COSMIC: COSV57597419;