rs10504684

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-78901383-C-A
• chr8-78901383-C-G
• chr8-78901383-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XR_007060971.1(MITA1):​n.1709C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MITA1	XR_007060971.1	n.1709C>A		non_coding_transcript_exon_variant	Exon 2 of 2
MITA1	XR_001745965.2	n.1225-32360C>A		intron_variant	Intron 1 of 2
MITA1	XR_001745967.2	n.3285-32360C>A		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>A		intron_variant	Intron 1 of 5
ENSG00000309889	ENST00000845018.1	n.257-9475G>T		intron_variant	Intron 3 of 3
ENSG00000309889	ENST00000845019.1	n.223-9475G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 90

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.88
DANN	Benign	0.71
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;