chr6-18138983-G-A

Variant names:

• chr6-18138983-G-A
• rs2842934
• NM_000367.5:c.474C>T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_000367.5(TPMT):​c.474C>T​(p.Ile158Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 1,611,978 control chromosomes in the GnomAD database, including 487,573 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.78 (45952 hom., cov: 32)
  • Exomes 𝑓: 0.78 (441621 hom.)
• Consequence: TPMT NM_000367.5 synonymous
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.171
• Publications: 50 publications found

Genes affected

TPMT (HGNC:12014): (thiopurine S-methyltransferase) This gene encodes the enzyme that metabolizes thiopurine drugs via S-adenosyl-L-methionine as the S-methyl donor and S-adenosyl-L-homocysteine as a byproduct. Thiopurine drugs such as 6-mercaptopurine are used as chemotherapeutic agents. Genetic polymorphisms that affect this enzymatic activity are correlated with variations in sensitivity and toxicity to such drugs within individuals, causing thiopurine S-methyltransferase deficiency. Related pseudogenes have been identified on chromosomes 3, 18 and X. [provided by RefSeq, Aug 2014]

ENSG00000307971 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 6-18138983-G-A is Benign according to our data. Variant chr6-18138983-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 356114.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.171 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000367.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPMT	NM_000367.5	MANE Select	c.474C>T	p.Ile158Ile	synonymous	Exon 6 of 9	NP_000358.1
	TPMT	NM_001346817.1		c.474C>T	p.Ile158Ile	synonymous	Exon 7 of 10	NP_001333746.1
	TPMT	NM_001346818.1		c.474C>T	p.Ile158Ile	synonymous	Exon 6 of 8	NP_001333747.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPMT	ENST00000309983.5	TSL:1 MANE Select	c.474C>T	p.Ile158Ile	synonymous	Exon 6 of 9	ENSP00000312304.4
	ENSG00000307971	ENST00000830125.1		n.268-10505G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118039 AN: 152030 Hom.: 45929 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.764

GnomAD2 exomes AF: 0.761 AC: 191319 AN: 251334 AF XY: 0.754

Gnomad AFR exome AF: 0.815

Gnomad AMR exome AF: 0.766

Gnomad ASJ exome AF: 0.720

Gnomad EAS exome AF: 0.779

Gnomad FIN exome AF: 0.752

Gnomad NFE exome AF: 0.786

Gnomad OTH exome AF: 0.763

GnomAD4 exome AF: 0.777 AC: 1133634 AN: 1459830 Hom.: 441621 Cov.: 47 AF XY: 0.772 AC XY: 560897 AN XY: 726330

African (AFR) AF: 0.810 AC: 27088 AN: 33446

American (AMR) AF: 0.764 AC: 34155 AN: 44704

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 18840 AN: 26116

East Asian (EAS) AF: 0.740 AC: 29388 AN: 39696

South Asian (SAS) AF: 0.644 AC: 55501 AN: 86182

European-Finnish (FIN) AF: 0.762 AC: 40721 AN: 53414

Middle Eastern (MID) AF: 0.719 AC: 4143 AN: 5760

European-Non Finnish (NFE) AF: 0.791 AC: 877651 AN: 1110176

Other (OTH) AF: 0.765 AC: 46147 AN: 60336

GnomAD4 genome AF: 0.776 AC: 118116 AN: 152148 Hom.: 45952 Cov.: 32 AF XY: 0.770 AC XY: 57229 AN XY: 74362

African (AFR) AF: 0.812 AC: 33723 AN: 41512

American (AMR) AF: 0.742 AC: 11336 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2497 AN: 3472

East Asian (EAS) AF: 0.760 AC: 3935 AN: 5180

South Asian (SAS) AF: 0.628 AC: 3029 AN: 4826

European-Finnish (FIN) AF: 0.742 AC: 7834 AN: 10564

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53190 AN: 67990

Other (OTH) AF: 0.762 AC: 1611 AN: 2114

Alfa AF: 0.782 Hom.: 203676

Bravo AF: 0.783

Asia WGS AF: 0.698 AC: 2428 AN: 3478

EpiCase AF: 0.778

EpiControl AF: 0.773

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2842934; hg19: chr6-18139214; COSMIC: COSV59429867;