rs638820

chr1-109667284-G-A

Variant summary

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

The XR_007059238.1(GSTM4):n.2100G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,046 control chromosomes in the GnomAD database, including 20,814 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 0.52 (20814 hom., cov: 31)
• Consequence: GSTM4 XR_007059238.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

GSTM4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTM4	XR_007059238.1	n.2100G>A		non_coding_transcript_exon_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.523 AC: 78947 AN: 150952 Hom.: 20792 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.523 AC: 79009 AN: 151046 Hom.: 20814 Cov.: 31 AF XY: 0.524 AC XY: 38664 AN XY: 73822

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.557

Alfa AF: 0.510 Hom.: 11690

Bravo AF: 0.535

Asia WGS AF: 0.573 AC: 1990 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.090
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs638820; hg19: chr1-110209906; COSMIC: COSV53981927; COSMIC: COSV53981927;