rs3885022

Positions:

• chr8-78815811-G-A

Variant summary

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

The ENST00000649603.1(MITA1):​n.403+10116G>A 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 0.115 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 ENST00000649603.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375914	XR_001745967.2	n.1224+10116G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MITA1	ENST00000649603.1	n.403+10116G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0909

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0151

Gnomad4 SAS AF: 0.0918

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.108

Alfa AF: 0.117 Hom.: 1459

Bravo AF: 0.112

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3885022; hg19: chr8-79728046;