rs1545298

chr8-78849601-C-T

Variant summary

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

The ENST00000649603.1(MITA1):n.403+43906C>T 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 0.595 in 151,940 control chromosomes in the GnomAD database, including 28,753 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 0.60 (28753 hom., cov: 30)
• Consequence: MITA1 ENST00000649603.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375914	XR_001745967.2	n.1225-1490C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MITA1	ENST00000649603.1	n.403+43906C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90350 AN: 151822 Hom.: 28706 Cov.: 30

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.595 AC: 90455 AN: 151940 Hom.: 28753 Cov.: 30 AF XY: 0.591 AC XY: 43870 AN XY: 74262

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.593

Alfa AF: 0.543 Hom.: 3974

Bravo AF: 0.612

Asia WGS AF: 0.624 AC: 2169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.64
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1545298; hg19: chr8-79761836;