rs11047892

chr12-25205099-T-Achr12-25205099-T-G

Variant summary

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

The NM_001001660.3(ETFRF1):c.*787T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0996 in 215,708 control chromosomes in the GnomAD database, including 1,542 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 0.10 (1135 hom., cov: 33)
  • Exomes 𝑓: 0.097 (407 hom.)
• Consequence: ETFRF1 NM_001001660.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

ETFRF1 (HGNC:27052): (electron transfer flavoprotein regulatory factor 1) Involved in respiratory electron transport chain. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETFRF1	NM_001001660.3	c.*787T>A		3_prime_UTR_variant	3/3	ENST00000381356.9
ETFRF1	XM_005253319.5	c.*787T>A		3_prime_UTR_variant	3/3
ETFRF1	XM_005253320.5	c.*787T>A		3_prime_UTR_variant	4/4
ETFRF1	XM_017018850.3	c.*787T>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETFRF1	ENST00000381356.9	c.*787T>A		3_prime_UTR_variant	3/3	1	NM_001001660.3	P1
ETFRF1	ENST00000557540.7	c.*787T>A		3_prime_UTR_variant	3/3	2		P1
ETFRF1	ENST00000553788.6	c.51+1092T>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15311 AN: 152026 Hom.: 1135 Cov.: 33

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.0837

GnomAD4 exome AF: 0.0971 AC: 6171 AN: 63564 Hom.: 407 Cov.: 0 AF XY: 0.0972 AC XY: 2867 AN XY: 29502

Gnomad4 AFR exome AF: 0.0229

Gnomad4 AMR exome AF: 0.0690

Gnomad4 ASJ exome AF: 0.0587

Gnomad4 EAS exome AF: 0.000322

Gnomad4 SAS exome AF: 0.110

Gnomad4 FIN exome AF: 0.272

Gnomad4 NFE exome AF: 0.130

Gnomad4 OTH exome AF: 0.0969

GnomAD4 genome AF: 0.101 AC: 15305 AN: 152144 Hom.: 1135 Cov.: 33 AF XY: 0.105 AC XY: 7835 AN XY: 74346

Gnomad4 AFR AF: 0.0223

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0969

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.0828

Alfa AF: 0.0696 Hom.: 114

Bravo AF: 0.0832

Asia WGS AF: 0.0390 AC: 137 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11047892; hg19: chr12-25358033;