rs4970776

chr1-109728835-T-A

Variant summary

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

The ENST00000431955.1(ENSG00000241720):n.249+2767T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,024 control chromosomes in the GnomAD database, including 15,627 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 0.44 (15627 hom., cov: 31)
• Consequence: ENST00000431955.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

Genes affected

(HGNC:):

GSTM5 (HGNC:4637): (glutathione S-transferase mu 5) Cytosolic and membrane-bound forms of glutathione S-transferase are encoded by two distinct supergene families. At present, eight distinct classes of the soluble cytoplasmic mammalian glutathione S-transferases have been identified: alpha, kappa, mu, omega, pi, sigma, theta and zeta. This gene encodes a glutathione S-transferase that belongs to the mu class. The mu class of enzymes functions in the detoxification of electrophilic compounds, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress, by conjugation with glutathione. The genes encoding the mu class of enzymes are organized in a gene cluster on chromosome 1p13.3 and are known to be highly polymorphic. These genetic variations can change an individual's susceptibility to carcinogens and toxins as well as affect the toxicity and efficacy of certain drugs. Diversification of these genes has occurred in regions encoding substrate-binding domains, as well as in tissue expression patterns, to accommodate an increasing number of foreign compounds. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 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
	ENST00000431955.1	n.249+2767T>A		intron_variant, non_coding_transcript_variant		3
GSTM5	ENST00000429410.2	n.82+16487T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67437 AN: 151906 Hom.: 15606 Cov.: 31

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.444 AC: 67499 AN: 152024 Hom.: 15627 Cov.: 31 AF XY: 0.443 AC XY: 32945 AN XY: 74328

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.439

Alfa AF: 0.421 Hom.: 1713

Bravo AF: 0.452

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970776; hg19: chr1-110271457;