rs8102334

Positions:

• chr19-51348475-G-A

Variant summary

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

The NM_001985.3(ETFB):​c.439-1417C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,948 control chromosomes in the GnomAD database, including 16,149 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 0.45 (16148 hom., cov: 31)
  • Exomes 𝑓: 0.38 (1 hom.)
• Consequence: ETFB NM_001985.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

Genes affected

ETFB (HGNC:3482): (electron transfer flavoprotein subunit beta) This gene encodes electron-transfer-flavoprotein, beta polypeptide, which shuttles electrons between primary flavoprotein dehydrogenases involved in mitochondrial fatty acid and amino acid catabolism and the membrane-bound electron transfer flavoprotein ubiquinone oxidoreductase. The gene deficiencies have been implicated in type II glutaricaciduria. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETFB	NM_001985.3	c.439-1417C>T		intron_variant		ENST00000309244.9
ETFB	NM_001014763.1	c.712-1417C>T		intron_variant
ETFB	XM_024451418.2	c.328-1417C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETFB	ENST00000309244.9	c.439-1417C>T		intron_variant		1	NM_001985.3	P1
	ENST00000600974.1	n.78+3229G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69080 AN: 151822 Hom.: 16146 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.439

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.455 AC: 69108 AN: 151940 Hom.: 16148 Cov.: 31 AF XY: 0.452 AC XY: 33585 AN XY: 74242

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.434

Alfa AF: 0.476 Hom.: 2850

Bravo AF: 0.445

Asia WGS AF: 0.226 AC: 789 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	2.4
DANN	Benign	0.18

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: rs8102334; hg19: chr19-51851729;