8-78840775-C-T

Variant names:

• chr8-78840775-C-T
• rs4739140
• ENST00000649603.2:n.517+35080C>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+35080C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,134 control chromosomes in the GnomAD database, including 41,288 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 0.72 (41288 hom., cov: 33)
• Consequence: MITA1 ENST00000649603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 7 publications found

Genes affected

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

LINC02605 (HGNC:53974): (long intergenic non-protein coding RNA 2605)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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+35080C>T		intron	N/A
	LINC02605	ENST00000565297.2	TSL:6	n.*250C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109887 AN: 152016 Hom.: 41231 Cov.: 33

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.723 AC: 110001 AN: 152134 Hom.: 41288 Cov.: 33 AF XY: 0.721 AC XY: 53592 AN XY: 74354

African (AFR) AF: 0.934 AC: 38808 AN: 41538

American (AMR) AF: 0.707 AC: 10801 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3470

East Asian (EAS) AF: 0.883 AC: 4559 AN: 5164

South Asian (SAS) AF: 0.601 AC: 2898 AN: 4820

European-Finnish (FIN) AF: 0.617 AC: 6517 AN: 10564

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42068 AN: 67988

Other (OTH) AF: 0.717 AC: 1514 AN: 2112

Alfa AF: 0.655 Hom.: 45552

Bravo AF: 0.741

Asia WGS AF: 0.759 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.76
PhyloP100		-0.80

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: rs4739140;

hg19: chr8-79753010;