7-116068511-T-G

Position:

• chr7-116068511-T-G

Variant summary

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

The ENST00000484212.5(TFEC):​c.198+42197A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,378 control chromosomes in the GnomAD database, including 23,469 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 0.55 (23469 hom., cov: 31)
• Consequence: TFEC ENST00000484212.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

TFEC (HGNC:11754): (transcription factor EC) This gene encodes a member of the micropthalmia (MiT) family of basic helix-loop-helix leucine zipper transcription factors. MiT transcription factors regulate the expression of target genes by binding to E-box recognition sequences as homo- or heterodimers, and play roles in multiple cellular processes including survival, growth and differentiation. The encoded protein is a transcriptional activator of the nonmuscle myosin II heavy chain-A gene, and may also co-regulate target genes in osteoclasts as a heterodimer with micropthalmia-associated transcription factor. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]

TFEC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TFEC	XM_011515963.2	c.198+42197A>C		intron_variant			XP_011514265.1
TFEC	XM_011515964.3	c.198+42197A>C		intron_variant			XP_011514266.1
TFEC	XM_011515965.3	c.198+42197A>C		intron_variant			XP_011514267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TFEC	ENST00000484212.5	c.198+42197A>C		intron_variant		2		ENSP00000417432.1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 83812 AN: 151260 Hom.: 23442 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.554 AC: 83888 AN: 151378 Hom.: 23469 Cov.: 31 AF XY: 0.556 AC XY: 41109 AN XY: 73976

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.580

Alfa AF: 0.506 Hom.: 7991

Bravo AF: 0.566

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.57
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1464776; hg19: chr7-115708565;