rs17159396

Variant names:

• chr7-30720445-G-A
• rs17159396
• ENST00000484180.1:n.246+22215G>A

Variant summary

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

The ENST00000484180.1(INMT):​n.246+22215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,248 control chromosomes in the GnomAD database, including 1,086 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 0.11 (1086 hom., cov: 32)
• Consequence: INMT ENST00000484180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

Genes affected

INMT (HGNC:6069): (indolethylamine N-methyltransferase) N-methylation of endogenous and xenobiotic compounds is a major method by which they are degraded. This gene encodes an enzyme that N-methylates indoles such as tryptamine. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream MINDY4 (aka FAM188B) gene. In rodents and other mammals such as cetartiodactyla this gene is in the opposite orientation compared to its orientation in human and other primates and this gene appears to have been lost in carnivora and chiroptera. [provided by RefSeq, Jul 2019]

ENSG00000290103 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375220	XR_001745154.2	n.490-21310G>A		intron_variant	Intron 1 of 2
LOC105375219	XR_927156.3	n.310+222C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INMT	ENST00000484180.1	n.246+22215G>A		intron_variant	Intron 1 of 3	1
ENSG00000290103	ENST00000702981.1	n.333+222C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16786 AN: 152130 Hom.: 1082 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0590

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.110 AC: 16805 AN: 152248 Hom.: 1086 Cov.: 32 AF XY: 0.112 AC XY: 8367 AN XY: 74436

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0589

Gnomad4 ASJ AF: 0.0793

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0909

Gnomad4 OTH AF: 0.0946

Alfa AF: 0.110 Hom.: 117

Bravo AF: 0.104

Asia WGS AF: 0.219 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17159396; hg19: chr7-30760061;