1-155609989-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000456382.2(ENSG00000232519):n.104-97G>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 0.00657 in 501,810 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.018 (90 hom., cov: 29)
  • Exomes 𝑓: 0.0017 (17 hom.)
• Consequence: ENST00000456382.2 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.11

Genes affected

(HGNC:):

MSTO1 (HGNC:29678): (misato mitochondrial distribution and morphology regulator 1) Involved in mitochondrion distribution. Located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 1-155609989-C-T is Benign according to our data. Variant chr1-155609989-C-T is described in ClinVar as [Benign]. Clinvar id is 1260671.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371452	XR_922171.2	n.77-97G>A		intron_variant, non_coding_transcript_variant
MSTO1	XM_047424007.1	c.-260C>T		5_prime_UTR_variant	5/18
MSTO1	XM_047424008.1	c.-260C>T		5_prime_UTR_variant	4/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000456382.2	n.104-97G>A		intron_variant, non_coding_transcript_variant		5
MSTO1	ENST00000697770.1	c.-378-1050C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0176 AC: 2684 AN: 152188 Hom.: 89 Cov.: 29

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00373

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.0129

GnomAD4 exome AF: 0.00174 AC: 609 AN: 349504 Hom.: 17 AF XY: 0.00150 AC XY: 275 AN XY: 183220

Gnomad4 AFR exome AF: 0.0567

Gnomad4 AMR exome AF: 0.00272

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000265

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000175

Gnomad4 OTH exome AF: 0.00371

GnomAD4 genome AF: 0.0176 AC: 2687 AN: 152306 Hom.: 90 Cov.: 29 AF XY: 0.0172 AC XY: 1282 AN XY: 74484

Gnomad4 AFR AF: 0.0623

Gnomad4 AMR AF: 0.00372

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000206

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.000284 Hom.: 0

Bravo AF: 0.0196

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.30
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs116421560; hg19: chr1-155579780;