7-30720445-G-A

Position:

• chr7-30720445-G-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:):

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/exons	MANE	Protein	UniProt
LOC105375220	XR_001745154.2	n.490-21310G>A		intron_variant
LOC105375219	XR_927156.3	n.310+222C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INMT	ENST00000484180.1	n.246+22215G>A		intron_variant		1
ENSG00000290103	ENST00000702981.1	n.333+222C>T		intron_variant

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;