10-58388024-G-A

Position:

• chr10-58388024-G-A

Variant summary

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

The NM_003201.3(TFAM):​c.221-166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,956 control chromosomes in the GnomAD database, including 23,009 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.53 (23009 hom., cov: 32)
• Consequence: TFAM NM_003201.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.180

Genes affected

TFAM (HGNC:11741): (transcription factor A, mitochondrial) This gene encodes a key mitochondrial transcription factor containing two high mobility group motifs. The encoded protein also functions in mitochondrial DNA replication and repair. Sequence polymorphisms in this gene are associated with Alzheimer's and Parkinson's diseases. There are pseudogenes for this gene on chromosomes 6, 7, and 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 10-58388024-G-A is Benign according to our data. Variant chr10-58388024-G-A is described in ClinVar as [Benign]. Clinvar id is 684187.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TFAM	NM_003201.3	c.221-166G>A		intron_variant		ENST00000487519.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TFAM	ENST00000487519.6	c.221-166G>A		intron_variant		1	NM_003201.3	P1
TFAM	ENST00000373895.7	c.221-166G>A		intron_variant		2
TFAM	ENST00000395377.2	c.165-166G>A		intron_variant		2
TFAM	ENST00000373899.3	n.491-166G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79942 AN: 151840 Hom.: 22983 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.527 AC: 80018 AN: 151956 Hom.: 23009 Cov.: 32 AF XY: 0.519 AC XY: 38515 AN XY: 74268

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.514

Alfa AF: 0.459 Hom.: 3400

Bravo AF: 0.546

Asia WGS AF: 0.420 AC: 1463 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

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10763537; hg19: chr10-60147784;