rs7816065

Variant names:

• chr8-78850423-C-T
• rs7816065
• ENST00000649603.2:n.517+44728C>T

Variant summary

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

The ENST00000649603.2(MITA1):​n.517+44728C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,816 control chromosomes in the GnomAD database, including 15,168 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 0.44 (15168 hom., cov: 31)
• Consequence: MITA1 ENST00000649603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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.517+44728C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67139 AN: 151694 Hom.: 15159 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.381

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.443 AC: 67182 AN: 151816 Hom.: 15168 Cov.: 31 AF XY: 0.442 AC XY: 32794 AN XY: 74174

African (AFR) AF: 0.387 AC: 16020 AN: 41420

American (AMR) AF: 0.469 AC: 7146 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3468

East Asian (EAS) AF: 0.690 AC: 3539 AN: 5132

South Asian (SAS) AF: 0.365 AC: 1759 AN: 4818

European-Finnish (FIN) AF: 0.453 AC: 4765 AN: 10520

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30986 AN: 67918

Other (OTH) AF: 0.454 AC: 957 AN: 2108

Alfa AF: 0.456 Hom.: 58708

Bravo AF: 0.446

Asia WGS AF: 0.523 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.83
DANN	Benign	0.46
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7816065; hg19: chr8-79762658;