8-78901383-C-G

Variant summary

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

The ENST00000649603.1(MITA1):n.404-32360C>G 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 0.214 in 139,360 control chromosomes in the GnomAD database, including 3,141 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 0.21 (3141 hom., cov: 30)
• Consequence: MITA1 ENST00000649603.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

Genes affected

MITA1 (HGNC:56733): (metabolism induced tumor activator 1)

LOC105375914 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375914	XR_001745967.2	n.3285-32360C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MITA1	ENST00000649603.1	n.404-32360C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.215 AC: 29875 AN: 139248 Hom.: 3141 Cov.: 30

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.214 AC: 29891 AN: 139360 Hom.: 3141 Cov.: 30 AF XY: 0.211 AC XY: 14366 AN XY: 68182

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.251

Alfa AF: 0.0772 Hom.: 90

Bravo AF: 0.203

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.90
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504684; hg19: chr8-79813618;