8-78901383-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MITA1	XR_007060971.1	n.1709C>G		non_coding_transcript_exon_variant	Exon 2 of 2
MITA1	XR_001745965.2	n.1225-32360C>G		intron_variant	Intron 1 of 2
MITA1	XR_001745967.2	n.3285-32360C>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MITA1	ENST00000649603.2	n.518-32360C>G		intron_variant	Intron 1 of 5
ENSG00000309889	ENST00000845018.1	n.257-9475G>C		intron_variant	Intron 3 of 3
ENSG00000309889	ENST00000845019.1	n.223-9475G>C		intron_variant	Intron 3 of 3

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 v4.3

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;