rs7007634

Positions:

• chr8-78807362-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649603.1(MITA1):​n.403+1667A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,184 control chromosomes in the GnomAD database, including 866 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 0.10 (866 hom., cov: 32)
• Consequence: MITA1 ENST00000649603.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

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

LOC105375914 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375914	XR_001745967.2	n.1224+1667A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MITA1	ENST00000649603.1	n.403+1667A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15604 AN: 152066 Hom.: 870 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.0793

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0580

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.102 AC: 15596 AN: 152184 Hom.: 866 Cov.: 32 AF XY: 0.101 AC XY: 7548 AN XY: 74412

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0792

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0568

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.101 Hom.: 390

Bravo AF: 0.101

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7007634; hg19: chr8-79719597;