chr8-78844356-C-T

Variant names:

• chr8-78844356-C-T
• rs2887502
• ENST00000649603.2:n.517+38661C>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+38661C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 151,954 control chromosomes in the GnomAD database, including 36,956 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 0.69 (36956 hom., cov: 31)
• Consequence: MITA1 ENST00000649603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 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+38661C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104200 AN: 151836 Hom.: 36907 Cov.: 31

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.686 AC: 104302 AN: 151954 Hom.: 36956 Cov.: 31 AF XY: 0.684 AC XY: 50801 AN XY: 74244

African (AFR) AF: 0.867 AC: 35950 AN: 41454

American (AMR) AF: 0.684 AC: 10435 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2059 AN: 3470

East Asian (EAS) AF: 0.849 AC: 4397 AN: 5176

South Asian (SAS) AF: 0.537 AC: 2584 AN: 4816

European-Finnish (FIN) AF: 0.603 AC: 6346 AN: 10524

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40458 AN: 67940

Other (OTH) AF: 0.678 AC: 1430 AN: 2110

Alfa AF: 0.621 Hom.: 15842

Bravo AF: 0.703

Asia WGS AF: 0.706 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.38
PhyloP100		-0.23

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: rs2887502;

hg19: chr8-79756591;