chr8-78901383-C-G

Variant names:

• chr8-78901383-C-G
• rs10504684
• XR_007060971.1:n.1709C>G

Variant summary

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

The XR_007060971.1(MITA1):​n.1709C>G variant causes a non coding transcript exon 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 XR_007060971.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.259 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MITA1	ENST00000649603.2		n.518-32360C>G		intron	N/A
	ENSG00000309889	ENST00000845018.1		n.257-9475G>C		intron	N/A
	ENSG00000309889	ENST00000845019.1		n.223-9475G>C		intron	N/A

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

African (AFR) AF: 0.264 AC: 8710 AN: 32978

American (AMR) AF: 0.193 AC: 2802 AN: 14530

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 899 AN: 3378

East Asian (EAS) AF: 0.169 AC: 854 AN: 5064

South Asian (SAS) AF: 0.182 AC: 862 AN: 4730

European-Finnish (FIN) AF: 0.151 AC: 1502 AN: 9974

Middle Eastern (MID) AF: 0.245 AC: 70 AN: 286

European-Non Finnish (NFE) AF: 0.207 AC: 13563 AN: 65598

Other (OTH) AF: 0.251 AC: 488 AN: 1944

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.90
DANN	Benign	0.58
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10504684; hg19: chr8-79813618;