rs3885022

Variant names:

• chr8-78815811-G-A
• rs3885022
• XR_007060969.1:n.9823G>A

Variant summary

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

The XR_007060969.1(MITA1):​n.9823G>A 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 0.115 in 152,012 control chromosomes in the GnomAD database, including 1,065 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 0.11 (1065 hom., cov: 32)
• Consequence: MITA1 XR_007060969.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 12 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MITA1	ENST00000649603.2		n.517+10116G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17419 AN: 151892 Hom.: 1070 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.0910

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0151

Gnomad SAS AF: 0.0930

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.115 AC: 17419 AN: 152012 Hom.: 1065 Cov.: 32 AF XY: 0.114 AC XY: 8483 AN XY: 74302

African (AFR) AF: 0.130 AC: 5396 AN: 41460

American (AMR) AF: 0.0909 AC: 1387 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3462

East Asian (EAS) AF: 0.0151 AC: 78 AN: 5164

South Asian (SAS) AF: 0.0918 AC: 442 AN: 4814

European-Finnish (FIN) AF: 0.113 AC: 1195 AN: 10566

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7977 AN: 67970

Other (OTH) AF: 0.108 AC: 228 AN: 2110

Alfa AF: 0.116 Hom.: 1823

Bravo AF: 0.112

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.75
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs3885022; hg19: chr8-79728046;