NM_001001660.3:c.-38+1217G>A

Variant names:

• chr12-25196554-G-A
• rs11047889
• NM_001001660.3:c.-38+1217G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001660.3(ETFRF1):​c.-38+1217G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0197 in 152,248 control chromosomes in the GnomAD database, including 59 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 0.020 (59 hom., cov: 32)
• Consequence: ETFRF1 NM_001001660.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETFRF1	NM_001001660.3	c.-38+1217G>A		intron_variant	Intron 1 of 2	ENST00000381356.9	NP_001001660.2
ETFRF1	XM_017018850.3	c.-7316G>A		5_prime_UTR_variant	Exon 1 of 3		XP_016874339.1
ETFRF1	XM_005253319.5	c.-38+1213G>A		intron_variant	Intron 1 of 2		XP_005253376.1
ETFRF1	XM_005253320.5	c.-146+1217G>A		intron_variant	Intron 1 of 3		XP_005253377.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ETFRF1	ENST00000381356.9	c.-38+1217G>A		intron_variant	Intron 1 of 2	1	NM_001001660.3	ENSP00000370761.4

Frequencies

GnomAD3 genomes AF: 0.0197 AC: 3001 AN: 152130 Hom.: 59 Cov.: 32

Gnomad AFR AF: 0.00497

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.00979

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0574

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0237

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0197 AC: 2996 AN: 152248 Hom.: 59 Cov.: 32 AF XY: 0.0213 AC XY: 1587 AN XY: 74424

African (AFR) AF: 0.00496 AC: 206 AN: 41538

American (AMR) AF: 0.0203 AC: 311 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00979 AC: 34 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.0573 AC: 276 AN: 4820

European-Finnish (FIN) AF: 0.0285 AC: 302 AN: 10594

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0237 AC: 1610 AN: 68026

Other (OTH) AF: 0.0232 AC: 49 AN: 2112

Alfa AF: 0.0232 Hom.: 168

Bravo AF: 0.0182

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.40
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs11047889; hg19: chr12-25349488;