8-78907881-A-G

Variant names:

• chr8-78907881-A-G
• rs7836241
• ENST00000649603.2:n.518-25862A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649603.2(MITA1):​n.518-25862A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,894 control chromosomes in the GnomAD database, including 26,619 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 0.58 (26619 hom., cov: 32)
• Consequence: MITA1 ENST00000649603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 2 publications found

Genes affected

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

ENSG00000309889 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649603.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MITA1	ENST00000649603.2		n.518-25862A>G		intron	N/A
	ENSG00000309889	ENST00000845018.1		n.257-15973T>C		intron	N/A
	ENSG00000309889	ENST00000845019.1		n.223-15973T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87308 AN: 151778 Hom.: 26570 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.576 AC: 87417 AN: 151894 Hom.: 26619 Cov.: 32 AF XY: 0.571 AC XY: 42385 AN XY: 74212

African (AFR) AF: 0.772 AC: 32022 AN: 41474

American (AMR) AF: 0.536 AC: 8168 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3468

East Asian (EAS) AF: 0.774 AC: 3980 AN: 5142

South Asian (SAS) AF: 0.445 AC: 2144 AN: 4816

European-Finnish (FIN) AF: 0.438 AC: 4606 AN: 10528

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32560 AN: 67928

Other (OTH) AF: 0.593 AC: 1247 AN: 2104

Alfa AF: 0.477 Hom.: 9808

Bravo AF: 0.595

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.56
DANN	Benign	0.40
PhyloP100		-0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7836241;

hg19: chr8-79820116;