1-109726566-C-T

Position:

• chr1-109726566-C-T

Variant summary

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

The ENST00000431955.1(ENSG00000241720):​n.249+498C>T 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 0.0584 in 152,286 control chromosomes in the GnomAD database, including 388 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 0.058 (388 hom., cov: 33)
• Consequence: ENST00000431955.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000431955.1	n.249+498C>T		intron_variant, non_coding_transcript_variant		3
GSTM5	ENST00000429410.2	n.82+14218C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0584 AC: 8883 AN: 152168 Hom.: 383 Cov.: 33

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0584 AC: 8897 AN: 152286 Hom.: 388 Cov.: 33 AF XY: 0.0591 AC XY: 4399 AN XY: 74452

Gnomad4 AFR AF: 0.0139

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.0328

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0583

Alfa AF: 0.0475 Hom.: 41

Bravo AF: 0.0594

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11101993; hg19: chr1-110269188;